In this paper, an exact reshaping method for the motor dynamics of a flexible-joint robot is proposed using an integral manifold approach. Obtaining the exact model for both motor-side and link-side dynamics of a flexible-joint robot is difficult due to its under-actuated nature and complex dynamics. Despite the simple structure of the motor-side dynamics, they are difficult to model accurately for a flexible-joint robot due to motor disturbances, especially when speed reducers such as harmonic drives are installed. An integral manifold feedback control (IMFC) is proposed to reshape the motor dynamics. Based on the integral manifold approach, it is theoretically proved that the IMFC reshapes motor dynamics exactly even with bounded disturbances such as motor friction. The performance of the proposed IMFC is verified experimentally using a single degree-of-freedom flexible-joint robot under gravity conditions.