In order to study the influence of electromagnetic (EM) effect and load change on the modal characteristics and dynamic response of gear transmission system driven by permanent magnet synchronous motor (PMSM), a electromechanical coupling dynamic model is established. The composite air gap permeability coefficient is introduced, and the formula of permanent magnet flux linkage under the influence of space harmonic and cogging effect is derived. The variation laws of gear meshing stiffness and bearing support stiffness under the influence of load change are simulated and analyzed. The natural frequency and vibration modal under different load, flux linkage and PI controller gain are revealed. On this basis, the influence of EM effect and load change on the resonance domain is analyzed through frequency sweep analysis and time domain simulation. Results indicate that the 1st order natural frequency and resonance amplitude will increase with the load, and the influence of PMSM EM excitation will gradually dominate. The increase of the flux linkage and speed loop controller gain Kpω will reduce the 1st order natural frequency. When Kpω =123, a new mode appears, and there is a modal transition between the new mode and mode 1 when Kpω =161. The research results can provide theoretical guidance for improving the transmission performance and structure optimization design of the permanent magnet gear transmission system.