The couple, who have nine children, rose to fame through the Channel 5 show which follows their life on Ravenseat Farm.
Despite their split, they will continue to work together on the farm and co-parent.
Last year they released a statement admitting they were experiencing a “rocky patch” in their marriage and asked for privacy.
They said in a joint statement posted on Ms Owen’s Instagram account, where she posts as Yorkshire Shepherdess: “Clive and I are sad to confirm that we have made the difficult decision to separate. This hasn’t been easy, but we both believe it’s the right choice for the future of our family.
“Although we are no longer a couple, we continue to work on the farm and co-parent together, with our number one priority the happiness and well-being of our children.
“We would like to thank everyone for their support and would ask that the media please respect our privacy as we work through this difficult time.”
It comes after the former couple released a statement in October 2021 following media speculation over the state of their marriage.
They said: “With the TV show and the books we’ve always aimed to show the reality of life on the farm, and just like any marriage we have our stresses and strains, coupled with all the complexities of what we do on the farm and bringing up nine kids.
“We’re a normal family and we’ve never said our marriage is perfect. Unfortunately the constant intrusion into our lives from the media has amplified a rocky patch that we’re going through.”
The couple asked for privacy “as we work through this”.
The couple run the 2,000-acre hill farm in Swaledale, North Yorkshire, and take care of about 1,000 sheep.
Our Yorkshire Farm first launched in 2018 and Ms Owen, 47, recently published a book titled Celebrating The Seasons With The Yorkshire Shepherdess, which features stories and pictures from their lives in the countryside, alongside seasonal recipes.
Additional reporting by Press Association