In order to improve the reliability of the five phase permanent magnet synchronous motor (PMSM) drive system, the five phase salient pole PMSM with the third order harmonic components in permanent magnet flux was studied. Based on fault free mathematical model, a fault tolerant direct torque control (DTC) strategy was proposed for two phase open circuit situation. The strategy constructed the α1β1 subspace voltage vector map of the five phase motor under two phase open fault, and selected the optimal voltage vector of the inverter output in the next cycle based on the fundamental subspace flux linkage information and torque information in the current cycle. In order to achieve smooth motor torque, the torque ripple caused by the third order harmonic flux linkage coupled to the α1β1 subspace was overcome by adding the torque feed forward compensation. The experiments showed that the proposed method could run smoothly under two phase open circuit and switch fast from normal to fault tolerant operation.