The invention discloses a three-phase four-wire system general electric energy quality controller and a control method thereof. A circuit topology structure of the electric energy quality controller comprises a power supply side circuit, and A, B and C three-phase power grid power supply ends Vsa, Vsb and Vsc are connected with the power supply side circuit; the power supply side circuit is connected with a load side circuit through a common bridge arm, the load side circuit is connected with series coupling transformers Ta, Tb and Tc to form a series compensation device, and the output of thecommon bridge arm is connected with a power supply neutral line N and neutral lines of converter sides of the series coupling transformers Ta, Tb and Tc through a filter inductor Lf7 at the same time; a three-phase compensation voltage is output to compensate a three-phase power grid voltage such that a load voltage is a three-phase constant, balanced and symmetrical sine voltage. A single energystorage capacitor structure is adopted, the capacitor capacity is small, the capacitor voltage fluctuation is low, and the loss is small; few power electronic devices are adopted, and the formed universal power quality controller is simple in circuit structure, low in manufacturing cost and high in efficiency; and the control method is simple and easy to implement.