There is provided an integrated control method for eliminating a low frequency ripple in a power conversion system for a fuel cell, more particularly, a control method of a power conversion system capable of eliminating a low frequency ripple, controlling a DC link voltage, and controlling an output power and a system using the same control method. A power conversion system (PCS) that converts an output of a DC power supply received from an external power supply includes a converter that converts a voltage of the input power supply; an inverter that converts an output voltage of the converter into an AC voltage; and a converter control module that outputs a PWM signal for controlling a switch of the converter, and after receiving a power instruction value, the converter control module generates the PWM signal for controlling the converter based on the power instruction value.