The dual three-phase permanent magnet synchronous motor (DTP-PMSM) has attracted attention due to its advantages, including reduced power inverter burden and torque pulsation mitigation during high-power operations. Its dual winding design allows us to use redundant controller strategies to improve the system’s reliability. however, in practical operation, it is common for the torque output of two sets of windings to be unbalanced, with the torque output of one set of windings gradually increasing while the torque output of the other set of windings decreases. This phenomenon not only increases the energy loss of the motor but may also shorten the motor’s lifespan. In order to effectively address this issue, this article delves into the working principle of PMSM and establishes a mathematical model for the DTP-PMSM speed control system based on the principle. Through this model, we further analyze the fault mechanism of unbalanced torque output and propose an improved design for the speed loop PI controller. Simulation experiment results show that this enhanced PI controller design can effectively solve the torque imbalance issue, significantly improving the stability and reliability of the DTP-PMSM speed control system. Such improvements are of great significance for enhancing motor performance and extending its lifespan.