A method of operating fuel cell system includes generating electricity by a fuel cell using fuel gas and oxidizing gas and allowing cooling water to flow in the fuel cell and thereby cooling the fuel cell. The method includes transferring moisture from exhaust gas to supply gas using a first humidifier, the exhaust gas being discharged from the fuel cell, the supply gas being supplied to the fuel cell, and transferring moisture from the cooling water to the supply gas humidified using a second humidifier. The method includes at least one of detecting humidity of the supply gas humidified, detecting temperature of the cooking water, detecting the flow rate of the supply gas and detecting the amount of electricity generated by the fuel cell. The method also includes controlling the humidity of the supply gas humidified based on the value detected.