There's No Place Like Home - S3-E22
Revealing mistake: After Snow White hugs Red Riding Hood goodbye, there is a wide shot where Snow walks toward Charming. If you look at her face, it it not Ginnifer Goodwin, but a body double. The body double's face can also be seen in the wide shot where Snow walks away. (00:19:20)
Answer: He knows who she is because he knows that the fairy tales are true. He was also shown to sneak out to go see Emma or someone else. Sometimes he succeeded, sometimes he didn't. This is how he knew to look for her despite his strict mother.