The eccentric singer wrote the track while the pair were still dating and she admitted that she gets emotional when she performs it.
She explained to US Weekly: "There is not one song on any of my records that wasn't written by me, and I think when you write your own music you find ways to reinvent [the songs] emotionally through yourself and performance so that they are different every night, and that song, you know, sometimes it's about the guys and sometimes it's about the fans."
GaGa also insisted that her "close connection" to her fans is the most important thing to her.
She added: "The greatest gift was that I would have such a close connection with my fans and that's the greatest accomplishment of my life so far.
"Truthfully, the greatest accomplishment in my career thus far is that I truly have a genuine, authentic and beautiful relationship with little monsters. That makes it all worth it."
GaGa's sophomore album Born This Way has become the fastest-selling of 2011 worldwide.
Listen to Lady GaGa perform 'You & I' on the Today show below: