For reducing the effect of flexibility, backlash and friction, which are brought by the harmonic gear, a kind of multiple loops’ control method is proposed based on double speed loops. Double speed loops consist of speed loop in motor side and speed loop in load side. The speed loop in motor side is the inner loop and the speed loop in load side is the outer loop. The paper separately analyses the control performance of single speed loop and double speed loops in theory. Finally, the experiment results are used to validate the effectiveness of the control method based on double speed loops for inhibiting the nonlinear deadzone in the harmonic drive system.