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Girlfriend Lauren Silverman ran to the judges' podium to hug him after he heard the show's next charity single, a cover of Snow Patrol's 'Run'.
It's not confirmed why he was crying, but the father is known for his charity work. He's even payed for surgery for children, as well as be involved with numerous hospices for young people.
Presenter Dermot O'Leary turned to Simon after the single had ended and asked what he thought of it, with dad-of-one Simon unable to speak. Lifting his glasses, he put his hand over his eyes and had a little cry.
Nicole Scherzinger put her hand on his arm to comfort him, with Lauren getting up on the podium and putting her arms around him from behind.
Realising the judge needed a minute to get himself together, Dermot swiftly moved on to the next segment while Simon consoled himself.
All the finalists - Max and Harvey, Jenny Ryan, V5 and winner Megan McKenna - recorded parts for the song, with a touching black and white video shown on the screen.
The video showed the finalists playing with the kids at Shooting Star House, a children's hospice that cares for babies and children with life-limiting conditions.
The song is available to buy now, with proceeds from the single going to charities Together For Short Lives and Shooting Star Children's Hospices.
It was announced earlier this year that for the first time the final would be a group effort rather than a solo effort.
Speaking to The Sun, Try Star's Ben Foden, 34, said: "Charity singles are always so iconic.
"It's a lovely memory for us to have but more importantly, we're all doing this for a fantastic cause."
Wes Nelson, 21, added: "We've seen some absolutely amazing charity singles over the years and to be part of that is surreal. It's something that makes a difference.
"Yes, X Factor was great and it meant a lot, but I think this is one of the most meaningful things you can do with music."
The massive two-hour long final for this year's programme aired on Saturday night and was won by former TOWIE star Megan McKenna.
The 27-year-old beat the others with performances of her own song 'This' and a cover of Leona Lewis's 'One More Sleep'.