Permanent magnet synchronous motors (PMSM) always suffer to disturbances of un-modeled dynamic and external world. This paper investigates the double-loop robust control of PMSM based on Hamiltonian system theory. First, the dynamic model of the PMSM is transferred to its equivalent Hamiltonian system model which can extensively present the physical property of the system. Then, in the inner loop we design a feedback controller to realize the assignment of structure matrix, Hamiltonian function and equilibrium point and to enhance the dynamic performance of the system. Finally, we put forward an outer loop robust controller to improve the robustness to external load disturbance. Simulation comparison with the traditional control scheme demonstrates the effectiveness of the proposed robust controller.