Provided is a method of controlling a manipulator system that includes a manipulator having an end effector and a joint portion and a manipulation input device with which a movement direction of the end effector can be input via a manipulation member, wherein the joint portion has a first joint, which is pivotable about a first axis parallel to a direction in which the end effector and the joint portion are arranged, and a second joint, which is positioned further on the distal-end side than the first joint is and which is pivotable about a second axis perpendicular to the first axis, the manipulator-system controlling method including a receiving step (S2) of receiving the movement direction, a rotating step (S3) of actuating the first joint based on the movement direction, a flexing step (S6) of actuating the second joint based on the movement direction, and a shifting step (S5) of shifting from the rotating step (S3) to the flexing step (S6) in accordance with changes in the magnitude of a physical amount of manipulation applied to the manipulation member.
