A control system for a flexible joint robot according to the disclosed present invention comprises: a dimension conversion unit for control input which receives a control input of a robot and converts the control input in the orthogonal coordinate system to the rotating coordinate system; an overall dynamics unit for flexible joint robot which receives the control input and a disturbance and outputs a control output by multiplying the control input, in which the disturbance is reflected, by at least one determinant; and a disturbance observer which calculates an estimated disturbance, which is an estimation of the disturbance, and reflects the estimated disturbance in the control input, wherein the disturbance observer comprises a reaction force removal unit including a determinant for removing the reaction force between the joints of the robot, a low-pass filter, and a dimension conversion unit for estimated disturbance.
