To be perfectly honest, you can’t really do anything.
What you’re asking here boils down to either, “How can I change my son so that he’ll be accepted?” or “How can I change the other kids so they’ll accept my son?” As much as you want to – and I love that you want to, because you love your kid and want everyone to understand how awesome he is – you can’t do either of these. You are in charge of your son, but you can’t be there all the time as he interacts with others, and you have no influence at all over other peoples’ children.
(As an aside, when I changed elementary schools due to bullying, my mother tried the first one. She had a whole list of things she forbade me to wear to the new school, among other random prohibitions. It didn’t make me any less weird or any less of a target, but it did make me feel like even my parents thought I was defective.)
What you can do is listen to your son. If he asks things like, “Why are they picking on me?” you can answer lovingly but honestly. Don’t tell him ‘they’re jealous because you’re smart/cool/unique’; tell him useful things like ‘people in general don’t like things they don’t understand, and they don’t understand your sense of humor’. I know I gave up on asking for advice after a while because all people would tell me was “be yourself”, without explaining to me that not all parts of “myself” were appropriate for all situations, and that the great thing about having all those different parts of “me” was that I could pick and choose which ones I wanted to use.
If you aren’t comfortable with negotiating this particular minefield, it might help if you can find him a counselor who is. I suggest finding one who is a huge nerd if at all possible – if you find one who comes off as having always known what was up socially, it might backfire and make your son feel too awkward to talk about anything relevant. Bonus if you can find one who is also experienced with helping kids on the autism spectrum, even if your son isn’t. It means they’ll have experience taking all those social things that other people just “know” and putting them into words that someone who’s used to tackling things in a geeky, detail-oriented, research sort of way can take apart and analyse.
You can also give him other places to be. It sucks being penned up for eight hours a day with people who don’t like you. It helps if he can look forward to going to another place with people who welcome him. Home, obviously, but being stuck at home all the time isn’t fun either. If you can find a club or a class for something he’s interested in, sign him up. Don’t worry if it’s not necessarily all kids his age – in fact, it might be better if it’s a place he’s unlikely to run into anybody who gives him guff at school. Sometimes kids who don’t get along with their peers will get along just ducky with an older mentor, or younger kids they mentor themselves.
And finally, keep an eye peeled for actual bullying going on. You cannot make the other kids like your son if they just don’t, but inappropriate behavior is something you can and should bring up with the people who are responsible for keeping your son safe at school. It doesn’t always work out what you might term well, but sometimes, if they absolutely refuse to behave with respect, it’s better if they just leave you the hell alone.