Disclosed are a grid-connected power conversion system and a control method thereof. The grid-connected power conversion system includes a fuel cell stack generating a DC voltage, a power conversion system (PCS) converting the DC voltage supplied from the stack into an AC voltage, a multi-input transformer including a primary coil having a plurality of voltage input terminals and a secondary coil transforming a magnitude of the voltage applied to the primary coil and outputting the transformed voltage, the plurality of voltage input terminals determining the number of turns of the primary coil differently from each other, one of the plurality of voltage input terminals receiving the AC voltage converted in the PCS, and a controller selecting the one of the plurality of voltage input terminals of the multi-input transformer based on the magnitude of the DC voltage generated from the stack and determining whether to replace the stack.