This paper proposes a new dead time compensation method of independent six-phase permanent magnet synchronous motors (IS-PMSM). The current of the independent phase machines contains odd-numbered harmonics because of the dead time and the nonlinear characteristics of the switching devices. By using the d-q-n three-dimensional vector analysis, these harmonics can be extracted at the n-axis current. Thus, the current distortion can be compensated by controlling the n-axis current of the IS-PMSM to zero. The proposed method is simple and can be easily implemented without additional hardware setup. The validity of the proposed compensation method is verified with simulations and several experiments.