The Canadian enjoyed his most successful year on tour to date under Moya as he moved into the top five in the world.
He reached his first ever Grand Slam final at Wimbledon in July but was eventually beaten by Andy Murray who won his second title at SW19.
Moya only joined Raonic's team in January and was expected to bring plenty of experience to the team.
Raonic is also coached by Riccardo Piatti on a full-time basis but the 25-year-old insists he and Moya will remain friends despite the split.
"We will no longer be continuing our coaching relationship, but remain close friends," he wrote on Facebook on Thursday.