Roig worked alongside the world number two's uncle and ex-coach Toni and more recently with Carlos Moya and Marc Lopez.
"It's been a pleasure and honour to work with Rafa and the rest of the team," Roig said in a statement. "We never thought we could get so many results and have such a long career with him but Rafa's a phenomenon and makes everything look easy."
Nadal, who has won 22 Grand Slam titles, described Roig as an important person in his career and thanked him for years of hard work and friendship.
"Francis is a great coach who knows tennis well and has helped me a lot to get better and better," Nadal said.
"I only have words of gratitude and I wish him all the luck in the world in his new project."
Nadal captured the Australian Open and French Open titles in an injury-plagued 2022 to top the list of men's Grand Slam title winners.
