A method for controlling a power conversion system includes: configuring a carrier period of the power modules, and configuring a phase shift of carrier waves of the adjacent power modules to be 2π/N; selecting M power modules to operate within the carrier period, where O≤M≤N, and providing a modulation wave to the power modules, an amplitude of the modulation wave being A/N of a carrier peak of the carrier waves; and comparing the value of the modulation wave with a value of the carrier wave of each of the power modules, respectively, wherein, when the value of the modulation wave is greater than the value of the carrier wave, the corresponding power module runs; when the value of the modulation wave is less than or equal to the value of the carrier wave, the corresponding power module stops.