In this article, a kind of position control method based on double speed closed loops is proposed to reduce turning error and nonlinear dead zone, which are caused by the flexibility and nonlinear friction in harmonic drive system. The speed loop of motor side is the inner loop and the speed loop of load side is the outer loop. Besides, the robustness performances of double speed loops and single speed loop are analyzed in theory, respectively. And it is stated that the performance of double speed loops is better than the performance of single speed loop. Furthermore, to further reduce the turning error and enhance the precision of system, the article puts forward applying double proportional-integral controllers with double extended state observers in the two speed loops. Extended state observers can transform the nonlinear models into an approximate linear model and eliminate the nonlinear frictions in the system. Finally, a few comparative experimental results show that the proposed control method has better performance for restraining the nonlinear features and enhancing the precision of the harmonic drive system.