An improved modulation model predictive control (MMPC) method is proposed to enhance the control performance and efficiency of the three-level indirect matrix converter-permanent magnet synchronous motor (TLIMC-PMSM) system, which suffers from the non-fixed switching frequency issue in model predictive control (MPC) and the heavy computational burden in traditional modulation model predictive control (MMPC). Firstly, the topology structure and principles of the TLIMC-PMSM system are introduced in detail. Secondly, the issues of the control system based on MPC and traditional MMPC are identified. Then, the improved MMPC method is proposed, which simplifies the sector selection method of the inverter level, adopts the improved output voltage prediction MMPC method, and modifies the inverter level value function. Finally, the experimental verification on the MATLAB/Simulink demonstrates that the TLIMC-PMSM system based on the proposed improved MMPC method exhibits superior control performance compared to the two traditional control methods.