Or, if it's habit you're referring to, you could say "Why does he eat so little?"

This question makes sense but it's worded in a weird way. It basically means "What type of food does he like the less." It would be worded better as "What doesn't he eat much of."

I should add, in English we would probably say something like "Why is he eating so little?" OR "Why isn't he eating anything?" (assuming I understand you correctly).

I think you mean to write "WHY doesn't he eat much."