The correlation between physical attractiveness and IQ is somewhere between insignificant and mildly positive, with a slightly higher correlation for men. The correlation between physical attractiveness and perceived intelligence is more significant.
There are typically two approaches to explain the (albeit mild) correlation:
Nature: From an evolutionary psychology perspective, one theory is that intelligent men are (on average) somewhat more successful, mate with more physically attractive women, resulting in offspring that are both more intelligent and more attractive than average. Evidence does support these assertions.
Nurture: However, there is an alternative explanation that accounts for these findings as an environmental (rather than hereditary) effect due to a self-fulfilling prophecy. According to this hypothesis, attractive children are perceived as more intelligent, resulting in more and better opportunities for them, that lead to better education, living standards, and ultimately higher intelligence.
The heritability of IQ, based on twin studies for example, is under some dispute, but suggests that both nature and nurture are significant factors, making both approaches equally valid. The debate may be resolved by examining cultures that don't associate physical attractiveness with intelligence (Eastern), but unfortunately, most of the research has focused on cultures that do (Western).