When the traditional modulation model predictive control (M2PC) is used in the three-level indirect matrix converter-permanent magnet synchronous motor (TLIMC-PMSM) system, there may exist the large fluctuation of motor operation and low quality of system waveform caused by the inaccurate sector selection and the duty cycle calculations of the M2PC. Aiming at the above problems, an improved modulation model predictive control based on the virtual vector prediction (VVP-M2PC) is proposed. Firstly, the mathematical model of the TLIMC-PMSM is established and the principle of the traditional M2PC is introduced. Secondly, the three-level inverter stage is improved with a new virtual vector and a new duty cycle calculation constructed to reduce the current control error and improve the waveform quality. Finally, compared with the simulation of the MPC control and the traditional M2PC control, the results show that the proposed algorithm is able to improve the speed, the torque ripple and the transient steady-state performance of the PMSM, improving the quality and robustness of the input and output waveforms of the system. © 2023 Power System Technology Press. All rights reserved.