There may be a neurological issue causing his eyes to cross. I came across this. I hope it helps.
https://answers.childrenshospital.org/tracking-...

Tracking the elusive genes that cause strabismus - Boston Children's Answers Tracking elusive strabismus genes, starting with esotropia - Vector blog

https://answers.childrenshospital.org/tracking-strabismus-genes/

@Emrahismayilov-when one of my twin granddaughters with autism was about 7 to 12, her eyes kept crossing and we were all worried about it. Doctors said that they would put a shunt in the child to address this issue, but we never did it. She is 24 now and the problem stopped for some reason and she does not wear eyeglasses. I wish I knew how this is supposed to be addressed medically, but the doctors never gave me a real answer.

I agree with @A MyAutismTeam Member. Vision therapy can make a huge difference. My NT son had binocular vision and vision therapy corrected that problem with all its symptoms (falling down, headaches, slow reading, etc).

And I also suggest you find a different eye doctor that specializes in young children. They should not "guess" on the strength of the glasses. That could really give him major headaches.

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A MyAutis...

Developmental optomatrist. We see one and are doing vision therapy because of reading problems and it is working. Muscles in the eyes can be worked on.

My son has the same issue. We discovered the eye issue before the autism. Hopefully you are seeing a pediatric opthalmologist. They have the means to see what is going on with your sons eyes through interactive play that can make the experience much less traumatic. Granted, there are times when you will experience screaming, throwing things and biting, but it's well worth it. Your son probably has amblyopia which can be from a muscle issue or from really poor eye sight. My son had horrible eye sight and was declared legally blind. We started with glasses (what a disaster that was). We had to move on to patching. Something to consider is chemical patching. You put drops in their eyes (I did that during naps) that dialates their eyes. It makes it so that they can only see if they wear their glasses. It made a HUGE difference for us. We had to do regular patching as well as his left eye completely stopped working. THAT was a NIGHTMARE, but we got through it. He now sees 20/40 in both eyes (which is a miracle in itself) with his glasses on. Prior to 6yrs of age, eye sight can be corrected. We made it by the skin of our teeth!