To suppress the harmonic components of the phase current of dual three-phase permanent magnet synchronous machines (DTP-PMSMs), an improved control strategy based on the multi-input multi-output (MIMO) proportional resonant (PR) controller is proposed in this paper. The control strategy includes the optimization of the controller and the integration of the voltage feedforward compensation method. By analyzing the traditional vector control strategy based on the vector space decoupling (VSD) coordinate transformation, an equivalent MIMO PR controller with parameter tuning is proposed, which can achieve no static error tracking for the alternating current (AC) signals. The controller considers the decoupling compensation in the traditional vector control strategy, which reduces the complexity of the system. The voltage feedforward compensation path includes the extraction of harmonic currents and the derivation of compensation voltage. By using feedforward compensation for specific harmonic components, more effective suppression of harmonic components can be achieved. Finally, the proposed control strategy was experimentally validated on the experimental platform. Compared with the traditional vector control strategy based on the VSD coordinate transformation, under the proposed control strategy, the total harmonic distortion (THD) content of the machine phase current was reduced by 6.12%, verifying the effectiveness and feasibility of the proposed strategy.