Permanent magnet synchronous motor(PMSM) works under the energy-limited condition in electric vehicle, so the iron loss impact on the drive system can’t be ignored. Therefore, the whole dynamic mathematical model and the port-controlled Hamiltonian model of PMSM considering iron loss are established firstly. Then the Hamiltonian stabilizing control of the PMSM drive system is realized by using the method of interconnection and damping assignment and energyshaping. Finally, the damping parameter impact on the convergence speed of rotating speed and the iron loss impact on rotating speed control are analyzed. The simulation results show that the proposed Hamiltonian control scheme can perform fast stabilizing of the drive system; the controlled drive system can effectively inhibit the load disturbance; considering the iron loss contributes to the further improvement of control performance and control precision.