The X Factor boss is reported to have stated that he "can't stand" the singer after seeing her as a coach on The Voice UK and hearing her making negative comments about his own shows.
Jessie J appeared as a guest judge on The X Factor UK last year, but has since described the show as "gimmicky".
"Simon used to really rate Jessie, both as an artist and as a person. Now he can't stand her," a source told The Mirror.
"He thinks her exploits during The Voice have killed off all credibility she had, not least when she slagged him off in interviews. Similarly, producers were livid about the comments she made about The X Factor, when she claimed the programme was gimmicky.
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"She had performed on the show so everyone is fuming. Simon will never work with Jessie again. And the show's execs feel she has made her BBC bed and must now lie in it. She wanted to plug her new single on this year's X Factor but Simon has said 'no'."
It was previously reported that Simon Cowell had tried to poach Jessie J from BBC One to become a permanent judge on The X Factor, but that she turned the offer down.
However, Jessie J told Digital Spy that she was still a fan of the "wonderful" X Factor earlier this year.
Watch Jessie J talk to Digital Spy about The Voice UK and The X Factor below: