The invention discloses a pure electric bus vehicle control unit (VCU) semi-physical simulation system and a control method thereof. The system comprises an upper computer, a signal interaction device, and the vehicle control unit (VCU), wherein the upper computer is used for building a bus model and correcting control parameters of the bus model to form a physical closed loop; the signal interaction device is used for transmitting data; the VCU is used for receiving the bus model data from the upper computer and processing the data; and the upper computer is in interaction connection with the VCU via the signal interaction device. The invention provides a complete solution scheme for pure electric bus VCU hardware detection, control strategy in-loop simulation, fault information search and parameter configuration optimization, a high-efficiency and low-cost VCU simulation verification method is provided for a designer, and a good start is provided for reducing the development difficulty for software and hardware of the pure electric bus VCU, enhancing safety, enhancing stability and the like.