“Thinking of you” is more commonly used to describe thoughts that come to your mind spontaneously. It can also be said when you are missing or sympathizing with someone. “Thinking about you,” on the other hand, is more often used to describe thoughts you have been focusing on for a while. It might show you have considered something more.

When he says he is thinking about you, it means he wants to see you again, among many other things of course. Something reminded him of you in a good and often sexual way. He's thinking if he tells you, you'll see it as a nice romantic gesture. He's trying to tell and show you that he's interested in you.