A medical device control system improves an inducing stability and operability of a medical device having its direction controlled with magnetism, which is used for the inspection or treatment in a subject's body. The control system is formed of a medical device including an insertion member inserted into the subject's body, and a magnetic field response portion disposed within the insertion member for generating torque in response to the magnetic field applied from outside the subject's body, a direction detection unit that detects an insertion direction of the insertion member, a user interface through which the information with respect to the control of the insertion direction is input and output, a magnetic field generation portion that generates a magnetic field that directs the insertion member to a control direction, and a user interface control unit that controls the user interface based on a discordance between the control direction and the insertion direction.