The invention discloses a determination method and system for electric energy quality comprehensive management. The method comprises the steps of obtaining three-phase current and three-phase voltagesine signals; obtaining an each-phase fundamental wave active current amplitude corresponding to each phase current; multiplying the each-phase fundamental wave active current amplitude and the three-phase voltage sine signals to obtain each-phase fundamental wave active current; obtaining each-phase idle harmonic current; obtaining a mean value of the each-phase fundamental wave active current amplitude; subtracting mean value of the each-phase fundamental wave active current amplitude from the each-phase fundamental wave active current amplitude to obtain an each-phase fundamental wave active current amplitude difference to obtain fundamental active current needing to the regulated; according to the difference between actual voltage and given direct current side voltage, obtaining voltage loop output through a proportional-integral controller; adding the fundamental wave active current needing to be regulated, the each-phase idle harmonic current and instruction current output by a voltage loop to obtain actual instruction current to perform the each-phase current balanced operation. By adopting the method, idle and harmonic wave in each-phase current are inhibited, and meanwhilethe balance of the three-phase current is achieved.