Ko was given the green light in October to become a full member of the LPGA Tour from the start of the 2014 season after the governing body waived the 18-year-old age limit clause.
Ko, who was born in South Korea and has already won five professional titles, four as an amateur, became the youngest winner on the LPGA Tour when she captured last year's Canadian Open at the age of 15.
She signed up with management company IMG earlier this month.
In statement to Fairfax media, Wilson said he was "incredibly disappointed" that their partnership had come to an end.
"We've spent a lot of time together over the past decade and during that time I've become very close to Lydia and her family. While I'm incredibly disappointed that our 11-year partnership is over, I respect Lydia and her team's decision," Wilson said in the statement.
"When I first met her the golf clubs were taller than she was and she didn't know the first thing about a driver or a putter but now she has one of the most envied swings in the women's golf world."
Media reports suggested Ko would now be coached by David Leadbetter in the United States.
Wilson began coaching Ko at six, where they were initially restricted by language difficulties as she had not yet been immersed in New Zealand schooling at that stage.
Ko had up to four lessons a week with Wilson, working from about 50 metres away from the green because anything else would have been too daunting, and he was amazed at the youngster's focus, motivation and ability to keep working at her game.
Wilson had told Reuters in October that Ko would not be out of place on the LPGA tour despite her youth.
"She is better than most of the people on the LPGA Tour. Her age does not match her skill set," he said.