The invention relates to a super capacitor energy storage type power quality compensator. A system structure comprises a compensation transformer, a series compensator, a parallel compensator, a super capacitor group, a current foldback circuit, a bidirectional DC/DC chopper circuit, a signal sampling circuit, a control circuit, a drive circuit, a human-computer interface and corresponding auxiliary circuits, which form a three-phase three-wire system topological structure. By utilizing the excellent characteristics of great power density, high charging and discharging speed and long cycle life of a super capacitor, the super capacitor energy storage type power quality compensator is matched with the DC/DC chopper circuit to form an energy storage control system which plays the roles of adjusting power and stabilizing the voltage of a direct current bus in work. The invention also has the functions of dynamic voltage recovery, active filter and reactive compensation and can ensure that a load can obtain rated sine voltage and the current of a grid is sine current with the same direction (unit power factor) with that of a voltage fundamental wave positive sequence active component, thereby comprehensively improving the quality of power. The invention has positive generalization and application value for both the public grid and users.