A medical manipulator system including an endoscope; a manipulator, the manipulator comprising a through-hole configured to hold the endoscope, wherein the manipulator is configured to move the endoscope; an operating unit configured to output an operating command; and a controller comprising one or more processors, the one or more processors configured to: acquire an image of the endoscope in a first configuration, the first configuration being a configuration of the endoscope at least partially inserted into the through-hole, the image comprising an inner surface of the through-hole; recognize a type of the endoscope based on the image; assign the endoscope to a recognized type of endoscope; receive an operating command from the operating unit; change the operating command based on the recognized type of endoscope to a changed operating command; and control the manipulator under the changed operating command.