The New York Post's Page Six cites a source who told the outlet the couple broke up following Instagram model Sydney Chase's April interview that she hooked up with Thompson. At the time, Thomspon denied the allegations.
Another insider added Khloe felt "betrayed" by Thompson amid the cheating rumours.
"Khloe really tried, but ultimately, felt too betrayed by him. She's done and says she will not go back."
The source added they are co-parenting but "are not romantically together".
Khloe had previously commented on her and Thompson's relationship in the final KUWTK reunion episode and spoke about how she regained trust with him.
"I know the growth and all the work that he's done, I know all of the help that he's gotten and the constant efforts that he makes every single day and how hard he fought to get back with me currently," the star said.