The 26-year-old Canadian appointed former Wimbledon champion Krajicek in December and reached two finals.
He failed to win a title, however, and lost in the last 16 of the French Open to world number 21 Pablo Carreno Busta.
"This decision has been a mutual one," Raonic said. "I would like to thank Richard for his help with my game, his dedication and professionalism."
World number six Milos Raonic has parted company with coach Richard Krajicek after only six months.