A method of controlling a manipulator system that includes a manipulator having an end effector and a joint portion and a manipulation input device for inputting a movement direction of the end effector by using a manipulation member, wherein the joint portion has a first joint being pivotable about a first axis parallel to an arrangement direction of the end effector and the joint portion and a second joint being pivotable about a second axis perpendicular to the first axis, in this order from a base side, the method including receiving the movement direction, rotating the first joint based on the movement direction, flexing the second joint based on the movement direction, and shifting from the rotating to the flexing in accordance with changes in the magnitude of a physical amount of manipulation applied to the manipulation member.
