Harley and Peter have been friends since childhood and reunited after the events in Mad Love. although he was aware of her past with the Joker, he wasn't about to give up on her, much like how Batman didn't give up on her either. He had also volunteered to help be her parole officer for her rehabilitation once she got out of Arkham and moved into the Talbot Hall boarding mansion house.
It is also revealed that she was Peter's first kiss while they were children.
As time went on, she later started to fall in love with him, and he with her, and her love became deeper after he saved her from one of Black Mask’s obsessive assassins: Talon of the Court of Owls, who was hoping to lure Alpha to kill him, and for recognizing her as Harley rather than the Joker’s girl or a criminal from Arkham. She and Peter both shared their first kiss in a long time with each other after her rescue, starting from that point on as boyfriend and girlfriend.
She often gets jealous when other girls flirt with or tempt him, even saying that Peter belongs only to her. She loves him very much and is willing to do anything with him. In response, Peter will do anything to protect her, as he loves her just as much as she loves him (unlike the Joker who just beats her up).
To add to that, Peter usually sleeps next to her naked. For this reason, she says that she has no problem with letting Peter see her naked and they even make love from time to time.