The Canadian player teamed up with the 1998 French Open champion in January and went on to reach his first Grand Slam final at Wimbledon, where he was beaten by Andy Murray.
The 25-year-old also rose to his highest-ever world ranking - third - after claiming 52 victories this season, but the partnership has now come to an end.
"Thank you to Carlos Moya for helping me tremendously this year, alongside my team, to get the best out of me," Raonic wrote on Instagram. "Under Carlos's direction and tutelage I have played my best yet to date.
"We will no longer be continuing our coaching relationship but remain close friends. I wish him all the best."
Raonic also worked with John McEnroe briefly during the season to help improve his form on grass and hard courts.