No, eye color can not affect the intelligence. The colors of the eyes are decided by the amount of pigments the iris contains in the eyes, which is in general inherited and which depends on the individual race. But the intelligence is decided by both the inborn conditions as well as the acquired dispositions. Therefore, it is wrong to say the eye color affects the intelligence.
Well, of course not. I do not think eye color will influence your intelligence. So you do not need to worry about it. In other words, we can say that eye color does not have any relation with one's intelligence. And in common, one's intelligence is related with the knowledge he have got and what he was born with. And for eye color, it can be very certain, for people are born with different certain eye color. And eye color will not affect our thinking ways, and also thoughts. So anyway, there is nothing to do with intelligence. So you do not need to think about it.