An apparatus for controlling a three-level inverter having two direct current -links for converting DC power generated in a plurality of photovoltaic modules into alternating current power, wherein one end of a first DC-link of the two DC-links is connected to a first potential point at which a first potential is generated in the plurality of PV modules, and one end of a second DC-link of the two DC-links is connected to a second potential point at which a second potential that is lower than the first potential is generated in the plurality of PV modules, and both the other end of the first DC-link and the other end of the second DC-link are connected to a third potential point at which a third potential having a medium level between the first potential and the second potential is generated in the plurality of PV modules, characterized in that: the apparatus further comprises two maximum power point tracking (MPPT) performing units for performing MPPT separately on each of the two DC-links to respectively generate DC-link voltage reference values; an arithmetic operation unit for performing a sum operation and a difference operation of each of the DC-link voltage reference values by receiving the DC-link voltage reference values output from the two MPPT performing units; a phase voltage referencing unit for generating each phase voltage reference value based on a value calculated by performing the sum operation of the arithmetic operation unit; a zero sequence voltage referencing unit for generating a reference value of zero sequence voltages based on a value calculated by performing the difference operation of the arithmetic operation unit; and a gate driving unit for generating a final reference value that is obtained by adding the reference value of zero sequence voltages calculated by the zero sequence voltage referencing unit to each phase voltage reference value of the phase voltage referencing unit and for applying a signal using the final reference value to each gate of the switching element of the three-level inverter. the apparatus further comprises two maximum power point tracking (MPPT) performing units for performing MPPT separately on each of the two DC-links to respectively generate DC-link voltage reference values; an arithmetic operation unit for performing a sum operation and a difference operation of each of the DC-link voltage reference values by receiving the DC-link voltage reference values output from the two MPPT performing units; a phase voltage referencing unit for generating each phase voltage reference value based on a value calculated by performing the sum operation of the arithmetic operation unit; a zero sequence voltage referencing unit for generating a reference value of zero sequence voltages based on a value calculated by performing the difference operation of the arithmetic operation unit; and a gate driving unit for generating a final reference value that is obtained by adding the reference value of zero sequence voltages calculated by the zero sequence voltage referencing unit to each phase voltage reference value of the phase voltage referencing unit and for applying a signal using the final reference value to each gate of the switching element of the three-level inverter.