When they fuck the first time he says that the scar on her neck is pretty and stuff and it looks like a crescent moon. Considering how they focused so much on that I’m thinking that the way he finds out is when he sees the scar when she's in her male outfit. But they already confessed their love to each other in the chapter where she leaves the dalia/camellia flower or whatever it is tied to a poem about their love being like a moons "shadow" in the way it doesn't exist during the day yada yada. In the way they describe it, the emperor feels a connection between her and the Yeon he knows. He thinks that they might be related or smth.. So I think he kinda thinks there might be something fishy going on..

Spoilers....
So I read the raws and I’m so impatient...GRRR when will she reveal her identity ahhhh I feel so bad for both of them...they just meet then fuck, then the girl leaves and the guy is heartbroken and the girl sees it in her “male” mode and she gets more heartbroken...LIKE BRO WHEN R U REVEALING THE TRUTH AGHHHH