A method for controlling a fuel cell vehicle includes acquiring a state data, deriving a mathematical voltage model by substituting the acquired state data into a voltage calculation formula, measuring a voltage of a fuel cell, approximating a mathematical voltage model to a measurement voltage and deriving the reaction area data when the mathematical voltage model approximates the measurement voltage, and controlling the system of the fuel cell vehicle based on the derived reaction area data to eliminate or prevent an over-humidification situation of the fuel cell.