A water removing system and method of a fuel cell vehicle using impedance are provided. The system measures measure the low frequency impedance of a fuel cell stack when a fuel cell system is stopped in a low temperature condition, and adjusts the air supply amount and supply time for removing the water supercharged into the fuel cell stack using the measured low frequency impedance. Thus, air is prevented from being unnecessarily supercharged into the fuel cell stack and at the same time, the water remaining in the fuel cell stack is removed.