A harmonic drive is compact torque transmission device with no backlash which is widely applied in industrial field to transmit torque precisely. However, one of the disadvantages of harmonic drives is the existence of mechanical flexibility caused by its structural properties, which imposes great limitation on designing precise controller This paper proposes a nonlinear controller for synchronous operation of DC servo-motors with harmonic drive, using Integrator Backstepping method. Furthermore, an alternative algorithm for serial type synchronous operation of multiple DC servo-motors is proposed. Simulation results by SIMULINK for proposed controller shows considerably small error and rapid approach to reference input, which can be adapted to industrial applications.