The invention discloses a parallel hybrid electric vehicle (PHEV) mode switching coordination control system based on interference compensation and a control method thereof. The control system comprises a driving module, a control module and a disturbance observer, and is simple and efficient, and close in logic. According to the control method, engine and motor torque errors, clutch friction torque errors, uncertainty of a system dynamics model, system modeling errors, elastic constants and damping coefficients of all parts and other factors are considered comprehensively, and the mode switching control system and the control method thereof based on the interference compensation are designed for the mode switching process, the interference observer is simplified to a low pass filter for interference compensation, and the control method is high in precision, simple and efficient, and is more suitable for promotion.