The invention discloses a low-voltage power distribution network electric energy replacement high-efficiency energy-saving control system and an application method thereof. The control system comprises a system optimization controller and a plurality of meter box-type energy-saving governing devices, wherein the meter box-type energy-saving governing device comprises a meter box body and an activecompensation unit which is arranged in the meter box body and has harmonic governance, reactive compensation and three-phase imbalance adjustment functions; the active compensation units are arrangedin parallel in a line of a transformer outgoing line end of a low-voltage power distribution network and a line tail end; and control ends of the active compensation units are respectively connectedwith the system optimization controller through a network. The system has the functions of harmonic governance, reactive compensation and three-phase imbalance adjustment, and the system optimizationcontroller serves as a core control unit of a coordinated control electric energy replacement high-efficiency energy-saving control system, so that ordered and high-efficiency operation of each meterbox-type energy-saving governing functional unit can be realized.