The traditional direct torque control (DTC) method will produce a larger harmonic current in the x, y subspace when applied to a dual three-phase permanent magnet synchronous machine (DTP-PMSM) because the voltage vector used for DTC is not equal to zero in the x, y harmonic subspace. To mitigate this problem, in this manuscript, a model predictive direct torque control (MPDTC) method is proposed to eliminate the harmonic current in DTP-PMSM. The spatial distribution characteristic DTP-PMSM voltage vector is analyzed; then, the table of vector group can be obtained according to DTC, and each vector group can be combined to obtain the zero-voltage vector in the x, y subspace. According to the cost function, MPDTC selects the vector group and obtains the optimal vector sequence combination to eliminate the harmonic current in the x, y subspace. Furthermore, the MPDTC achieves closed-loop control of harmonic currents in the x, y subspace. The MPDTC can also eliminate harmonic currents caused by other factors. The simulation results show that the method of MPDTC can effectively suppress the harmonic current of DTP-PMSM.