That would mean he respects you....your intelligence, your morals, your sense of fairness, etc.
If a guy says he thinks highly of you, it likely means that he has a positive opinion of you and respects you. He may admire your qualities, values, or behavior.
When someone thinks highly of you, they respect you. They think good things of you and admire your words and actions. They hold you in high regard. It's a compliment.
He thinks your awesome
It implies that the guy thinks you are gay.
That that girl thinks that that guy is handsome.
He thinks you are a hard worker.
It means he thinks you are attractive.
it means that he likes you and he thinks your nice
He thinks you are quite sexy.
If a guy says he thinks you are the prettiest girl on the school campus, it means that he likes you.
It seems he thinks highly of you, enjoys your company and friendship.
He likes you, thinks you are cool.
He likes you, just like he thinks, you like him!
It means he want to know if you think about him because he thinks about you!