My honest advice is to seek assistance of a medical professional. This might not be related to the game.

Yes, as I said:  

@guerringuerrin I tried this ffm_mod, but i didn't notice change. As I can see it's just for colors, not graphics itself.

Oh i never understood what Vsync is for. Tried it now.... It goes above 60, but drops to 40-50 due to PC performance. But it doesn't help. Just spectated game for 5 mins and my eyes are already tired. Maybe b/c of playing other settings... i have to set to low quality and then it's pixelated. But idk, i didn't have such problem with Minecraft years ago...

Could you try enabling VSync? It disables screen tearing and ignores FPS limiting, though it won't go over your monitor frequency (typically 60Hz).