The invention discloses a zero-sequence current suppression method based on a five-phase open-winding fault-tolerant fractional-slot concentrated winding interior permanent magnet (FTFSCW-IPM) motor drive system. In the operating process of a motor, the zero-sequence current of the motor is adjusted by a PI (Proportional Integral) adjustor to obtain a reference value of common-mode voltage, then the acting time of zero voltage vectors of two inverters is controlled according to the obtained reference value of common-mode voltage so that the switching sequences of the two inverters work in staggered time, and corresponding reference common-mode voltage vectors are synthesized to suppress the zero-sequence current. The method is relatively simple to implement and low in requirement for a controller, can be conveniently transplanted to other direct-current buses, and meanwhile, can suppress the zero-sequence current caused by common-mode voltage, well suppress the zero-sequence current caused by dead areas of the inverters and reduce the harmonic component of the current.