Earlier this month, Thompson, 30, confirmed that he fathered a child with Maralee Nichols, the woman suing him for child support and other pregnancy-related fees, while he was publicly dating Kardashian.
Though this isn't the first time that Thompson has been involved in a cheating scandal while dating the Keeping Up with the Kardashians alum, a source tells PEOPLE that Kardashian, 37, is having a tough time accepting the recent paternity drama.
"Khloé is really struggling with what's happening with Tristan," a source says. "This time that he was unfaithful has been much harder than the previous times. She really wants the relationship to work and she has been devastated."
"She's leaning heavily on Kris all of the time. But Kris wants Khloé and Tristan to be in a good place so she's encouraging Khloé to keep the lines of communication open," the source continues of Kardashian and Thompson, who share 3½-year-old daughter True.
"[Khloé] wanted the fairytale life with him and she's so upset," the source adds. "People around her have never seen her so down and are so thankful she has her mother there who has barely left her side."
Khloe Kardashian/Instagram Khloé Kardashian and Kris Jenner
On Jan. 3, Thompson posted a message on his Instagram Story confirming that he is the father of Nichols' son, who was born Dec. 1, after previously disputing the child's paternity. (Thompson also shares son Prince, 4, with ex-girlfriend Jordan Craig.)
"Today, paternity test results reveal that I fathered a child with Maralee Nichols," the NBA player wrote. "I take full responsibility for my actions. Now that paternity has been established I look forward to amicably raising our son."
"I sincerely apologize to everyone I've hurt or disappointed throughout this ordeal both publicly and privately," he continued.
On a second Instagram Story slide, Thompson apologized to Kardashian, writing, "Khloé, you don't deserve this. You don't deserve the heartache and humiliation I have caused you. You don't deserve the way I have treated you over the years. My actions certainly have not lined up with the way I view you. I have the utmost respect and love for you. Regardless of what you may think. Again, I am so incredibly sorry."
Kardashian and Thompson had an on-and-off relationship for years before splitting most recently in June. The Good American mogul has not yet commented on Thompson's third child.
A source told PEOPLE earlier this month that Kardashian has already moved past the drama to focus on herself, and on co-parenting True.
"She wants the new year to be different," the source said at the time. "She wants to focus on her own happiness."
The source added: "But her family knows that she will meet the right guy when she is ready. It's hard for her family when she is upset. They love her so much. Khloé is such a strong person though. She has already moved on after finding out that Tristan was expecting another baby."