An apparatus for managing a battery system comprising battery units having different outputs and capacities, the apparatus comprising: a power measuring unit configured to measure the magnitude in watts of a charge power supplied to a battery system or a discharge power output from the battery system; a reference setting unit configured to variably set a power distribution reference in watts according to the measured magnitude of power by using a frequency filter, to obtain a filtered result value for the measured value of the charge power or discharge power, so that when the measured power varies with time, the reference setting unit sets the power distribution reference differently with time; and a power distributing unit configured to determine, according to the set power distribution reference, charge or discharge power sharing ratios respectively for the battery units having different outputs and capacities, to distribute and supply the charge power sharing ratios to said battery units or allow the discharge power sharing ratios to be distributed and output from said battery units. wherein the battery system includes a high-output battery unit having a high output and a low capacity and a high-capacity battery unit having a high capacity and a low output, and wherein the power distributing unit distributes the charge or discharge power lower than the power distribution reference to the high-capacity battery unit and the charge or discharge power higher than the power distribution reference to the high-output battery unit, the reference setting unit setting the power distribution reference such that the high-output battery unit is used equal to or less than a first predetermined percentage of the total operating time of the battery system and such that the high-output battery unit is used with equal to or less than a second predetermined percentage of the total operating power of the battery system. a power measuring unit configured to measure the magnitude in watts of a charge power supplied to a battery system or a discharge power output from the battery system; a reference setting unit configured to variably set a power distribution reference in watts according to the measured magnitude of power by using a frequency filter, to obtain a filtered result value for the measured value of the charge power or discharge power, so that when the measured power varies with time, the reference setting unit sets the power distribution reference differently with time; and a power distributing unit configured to determine, according to the set power distribution reference, charge or discharge power sharing ratios respectively for the battery units having different outputs and capacities, to distribute and supply the charge power sharing ratios to said battery units or allow the discharge power sharing ratios to be distributed and output from said battery units. wherein the battery system includes a high-output battery unit having a high output and a low capacity and a high-capacity battery unit having a high capacity and a low output, and wherein the power distributing unit distributes the charge or discharge power lower than the power distribution reference to the high-capacity battery unit and the charge or discharge power higher than the power distribution reference to the high-output battery unit, the reference setting unit setting the power distribution reference such that the high-output battery unit is used equal to or less than a first predetermined percentage of the total operating time of the battery system and such that the high-output battery unit is used with equal to or less than a second predetermined percentage of the total operating power of the battery system.