This paper proposed a new fault-tolerant control strategy focusing on phase-loss (PL) fault based on winding's Y/Delta change and phase shift under vector control in electric vehicle driving system with a new flux-modulated permanent magnet compact in-wheel (FMPMCW) motor. The winding is connected in star connection in normal operation and delta connection when fault occurs in which a new phase-shift fault-tolerant scheme is proposed. The proposed strategy has the advantages of the simplicity of fault detecting and fault-tolerant program, symmetrical three-phase sinusoidal inverter current, little size of driving system, and low cost of investment. Simulation and experimental verification of the fault-tolerant control strategy show that the FMPMCW motor driving system can switch from the fault state to the FT operation smoothly.