It is a common expression. I'd explain it as not only too complicated, but the person is saying that it is too complicated for them, they are not smart enough, or not skilled enough, to understand, or to appreciate it. It is as though someone is in too deep water: it is over my head.

The literal meaning is "it is located above my head." The figurative meaning is "I don't understand it." It sounds like the boy didn't understand the picture.