Your sentence is understandable, but it could be rephrased slightly to sound more natural and concise. Here's a better version: "Good thinking skills can make a student the top of their class." Or, more conversationally: "Good thinking skills can help a student become the top in their class." This makes the meaning clearer while maintaining a natural tone. Also, using "their" instead of "his" makes the sentence gender-neutral, which is more common in modern English.

I would say "thinking habits" rather than "skills". A skill is something specific.

Good thinking skills put a student AT the top of his class. Here the preposition AT is used to refer to a location/position/place, for example, at the top or at the bottom of something.

‘Ok’, yes, but a little awkward and imprecise. Good thinking skills are enough to be a top student. In this class, merely having good thinking skills will make him the top student. (Emphasizing that it’s a class of weak students) Having good thinking skills usually suffices to make a student stand out. Note that ‘good thinking skills’ is vague without context.