Kardashian, 40, filed for divorce in February and is seeking joint custody of their four children.
The famous family haven’t spoken much in public about the split, but family matriarch Jenner, 65, addressed her daughter’s divorce for the first time during an appearance on Australian radio programme The Kyle & Jackie O Show.
She said: “I think it’s always going to be hard anytime, you know, there’s a lot of kids.
“The good thing about our family is that we are there for each other and supportive and we love each other very, very much, so all I want is for those two kids to be happy. And I want the kids to be happy. That’s the goal.”
The final series of Keeping Up With The Kardashians, the reality TV show that made the family famous, began airing in the US on Thursday.
It featured Scott Disick claiming former girlfriend Sofia Richie made him choose between her and his ex-partner Kourtney Kardashian.
TV personality Disick, 37, has three children with Kourtney, 41, and had been dating Richie – the 22-year-old daughter of singer Lionel – since 2017.
They broke up last year. On the show it was revealed tensions between Disick and Richie emerged over his closeness to Kourtney.
“I thought I would give it a try and make her more of a priority, but then even when doing that, I feel like she just started wanting to push Kourtney out,” he told Kim and Khloe Kardashian.
“And I said like, that’s the most important thing to me is my kids and that’s my family, and the only family I have, including you guys along with it.
“She was like, ‘I don’t want to share you as a boyfriend with Kourtney. And then she literally said with an ultimatum: ‘You have to choose me or Kourtney.’”
Disick, father to sons Mason, 11, and Reign, six, as well as daughter Penelope, eight, said he will “never” give up his relationship with Kourtney.
He added: “Nothing in a million years will be worth what we have.”
Elsewhere in the show, Khloe, 36, spoke of her attempts to conceive a second child with professional basketball player Tristan Thompson.
The couple, who were not together at the time of filming but have since reconciled, already have a two-year-old daughter, True. They are trying for another child.