Dumbledore offers one theory at the end of Order of the Phoenix: Voldemort based his decision on blood purity, which is one of the only things he would have known about both of the boys, and which he can compare against his own:
“But he might have chosen wrong!” said Harry. “He might have marked the wrong person!”
“He chose the boy he thought most likely to be a danger to him,” said Dumbledore. “And notice this, Harry. He chose, not the pureblood (which, according to his creed, is the only kind of wizard worth being or knowing), but the half-blood, like himself. He saw himself in you before he had ever seen you.”
— Order of the Phoenix, chapter 37 (The Lost Prophecy)
J.K. Rowling confirmed in an interview that this wasn’t just a theory; this was the main reason that Voldemort went after Harry:
Why did Voldemort pick Harry and not Neville?
Dumbledore explains this in Order of the Phoenix. Voldemort identified more with the half-blood boy and therefore decided he must be the greater risk.
