I meditate with my eyes closed, but my eyes seem to unconsciously follow the body parts I'm scanning my body to feel for sensations and seems to give me a headache. Is it anyway to practice to stop this habit or so?

After doing two months of body scan, I stop doing it. It gave me headache, causes sweat, unconscious changing physical posture, and morph a calm mind into noisy mind during the meditation session.

There are many other vipassana. Others will argue with me, but I call it equanimity meditation.

You can follow Culadasa. He teaches samatha/vipassana. You can download Insight Timer and join a discussion group by his book title. The Mind Illuminated. You learned anapanasati. You just need to learn to have awareness instead of just focusing on your nostril area

It is far more effective than body scan.

Yea I usually go back to anapana after awhile. I'm going to look into your recommendation thank you. I'm glad I'm not the only one with this problem nobody else in my class seem to have this problem.

http://www.theepochtimes.com/n3/1975608-gamma-waves-and-inspiration-how-is-your-brain-vibrating/

Insight is your aha moment which comes about in gamma wave domain.. Culadasa teaches anapanasati except he teaches you to have introspective awareness while you have attention on breathing. You can YouTube his video.

It has been shown that awareness meditation induces gamma wave which yields insight. 

You mindfully breath while maintaining awareness of your posture and mind. This is the way anapanasati should be taught. Buddha taught anapanasati as mindfulness breathing meditation not concentration meditation. Once the mind is tranquil you can observe, which is vipassana.

The body image distortions are possibly showing up for you as classic mind & body 1st nana insight territory (see MCTB2).
http://www.dharmaoverground.org/dharma-wiki/-/wiki/Main/MCTB+1.+MInd+and+Body

I find this territory fascinating, and its fun to observe what the mind does when one widens the area of focus so that one incorporates, for example, the feeling of the back of the head and/or the ears whilst you feel half of your face melting! Take your time and observe carefully...play, experiment! Sankara's are involved. See for yourself!

With regards the eyes following the mental focus and the headache, if I understand you correctly, I have found this so far to be two linked issues:

The first issue is how one navigates and focuses in the feeling realm. If one is visually dominated/led, then it might be one utilises a visual metaphor to navigate and focus in the feeling realm. To 'see' if this is the case for you, examining in detail the mind & body nana as suggested above would be good first step methinks. The habitual use of a visual metaphor, to 'look around' for feelings in a particular body area and 'to focus in'
on a particular feeling may unconsciously recruit the physical eyes in the process i.e. eyes physically 'look around', and eyes focus muscles contract 'to focus in'. This is rather like one might at times unconsciously recruit the throat muscles while utilising the internal voice. i.e. a feeling/kinaesthetic metaphor to manipulate the internal voice.

The second issue is habitual tension/mental stress. In my case I was carrying alot of habitual tension in the head and eyes on top of which attempting to feeling focus added further tension to the eyes and head which would lead to head aches, general stiffness, feeling like crap etc. Whereas others, were perhaps not carrying so much habitual tension (particularly in the eyes and head), and so the addition of the technique didnt bust the comfort threshold and lead to headaches etc.

Out of the two issues I think the second one is the lowest hanging fruit and probably if dealt with sufficiently will in most circumstances alleviate the headaches and excess unnecessary discomfort and noisiness which can arise while pursuing techniques such as body scanning and breath meditations which have a narrow focus (on the nostrils, the hara etc) as skillful means for ones purpose.

Iam fairly confident of this, as a significant proportion of people, if not the majority, are visually dominated/led and probably employ a visual metaphor, unconsciously at times recruiting the physical eyes, to navigate and focus, yet they dont accrue enough tension/stress for it to be an issue for them. Thus I have not read much on this topic (eyes following observing) as a problem. I do recall a MCTB third pather describing his experience of meditating where clearly his eyes/head were being recruited/utilised in focusing on bodily feelings, yet it wasnt a source of headaches, problems etc, only curiosity.

To suggest an approach to your question:
"Is it anyway to practice to stop this habit or so?"

Is to figure out how to relax, the head and eyes particularly. This isnt directly related to the progress of insight paths, it appears to be mostly a silla/samatha issue. However to help shed fundamental tensions/mental stress classical insight is required. The silla aspect is to try and make sitting as pleasant as possible, by taking the time to figure out how to shed unnecessary tension...so adding tension by pursuing particular techniques is no big deal, just something to be curious about.

An additional secondary approach might be to try and condition yourself to navigate and focus in the feeling realm without drawing in the visual metaphor. Recently Ive been experimenting with 'nyasa', a tantric version of body scanning where one uses external causes to focus attention, such as ones own hands. So to scan the hand and arm, adopt a passive mental attitude and use your other hand to feel up and down the arm, whilst having utterly relaxed eyes and notice what happens.... play around with it!! Let me know!

best wishes...

ps
This thread is about the same issue:
http://www.dharmaoverground.org/discussion/-/message_boards/message/6030602

So long as you're noticing  what's happening in the foreground of attention (i.e the area of scanning or current phenomena being noted), it doesn't matter what's happening in the background. If the sensation of your eyes moving or any associated strain becomes primary in attention, then clearly observe the physical sensations in this area. 

At the beginning of practise we can often:

• Feel like we're observing our body "from somewhere": When this happens, notice that where we appear to be centered and observing from is just a cluster of sensations e.g. the sensations of muscular tension in the head and rapid moving of the eyeballs. By all means carry on your scanning practise 99% of the time, but something I found useful as a pragmatic tool was (a) to ask myself "where is my centre right now?". (b) use this to go to what seemed like my centre, or the place from "where" I was focussing attention (c) investigate this area to confirm that there is only a constellation of physical sensations that temporarily seem to give a sense of centrality, but with no sense of self in any of them. 
  
  
• Develop habits of strain/tension around the attempt to focus attention on an area: A lot of these habits simply resolve over time, but one tip is to make sure we try to include all tension/strain within scanning/noting. Even after hundreds of hours of practise, it's very easy to overlook subtle aspects of straining/tension e.g. a very subtle feeling of contraction around the periphery of the head or the body. It's overlooked because it's illusorily associated with the activity of attention and felt to constitute self, rather than just being noticed as yet more arising, impermenant phenomena. 
  
  
• Develop the idea that we need to block out everything to observe something: A lot of the strain associated with focussed attention is because we're trying to exclude everything except the object of attention. Replace this with the idea of foreground and background. It doesn't matter what you're aware of happening in the background (including eyes moving, orthat you're scratching an itch or whatever), so long as you have clarity with whatever's arising in the foreground of attention. It's easy to imagine that there is just one laserbeam-like ray of attention shining on stuff, but it's not true. When you're reading this post, your attention is mostly focussed upon the visual aspects of the text/screen and the mental aspect of comprehension, but there's also an enormous amount of sensory data being processed in the periphery e.g. the sight of the room, the sounds outside, the feeling of the chair, etc. You're aware of these things outside of your task, but they do not detract from focus. This happens perfectly easily without any specific attempt to exclude everything happening in the background. Likewise, in meditation, it's fine to notice stuff happening like the eyes moving around in the background, so long as you're investigating the current area of attention in the foreground. 

In general, stuff like this tends to work itself out over time and it doesn't matter if some phenomena in our experience seem to correlate or arise persistently. What's important is to notice the current arising phenomena with increasing clarity, speed and steadiness and investigate them with respect to the 3 characteristics. 

Justin - as soon as you become aware that your eyes are moving, stop. It will take practice. You have a lifelong habit to break.

Also you can slightly open your eyes for a few moments. 

Try different speeds. For me it is harder to keep them stationary when I scan fast.

Widen the area of awareness. I just do this for a few moments.

Just keep it up. Even if you don't totally break the habit, it will lessen and you will strengthen.