This idiom or expression means:

Too difficult, or complicated for one to handle.
Too much for one to handle. (If used with “in”.)

A. Did you understand the problem?
B. No, it was way over my head.

A. You’re in over your head. You should hire someone to help you.
B. No, I can do it. I just need a little more time.

Another meaning.
Going outside the chain of command.

A. I hear your supervisor is mad at you because you went over his head.
B. Well, he kept putting off my promotion. I had to talk to the director directly.

Also see:
Biting off more than one can chew.