Aiming at the problem of increasing the output torque of the dual three-phase permanent magnet synchronous motor (PMSM), the control principle of the 3rd harmonic current injection into the motor phase current and back electromotive force (EMF) is analyzed. The motor drive system is optimized, and the 3rd harmonic current is adjusted to solve current interference problem of two sets of windings. On the basis of the optimal phase current, a permanent magnet shaping method is proposed, which comprehensively considers the stator cogging effect, iron core saturation and magnetic leakage between tooth tips and poles, and the optimal quasi-sinusoidal back EMF is obtained. The output torque of the motor is increased by 18.1% due to the interaction of quasi-sinusoidal current and quasi-sinusoidal back EMF. Finally, the correctness of the theoretical derivation is verified through finite element analysis and experiments, which provides technical support for the large-scale application of high reliability dual three-phase PMSM.