A cold start control method and system for fuel cell vehicles determines when the fuel cell vehicle is started, whether the fuel cell vehicle enters a cold start mode. An estimated time estimated to be required until the stopped vehicle coolant temperature, which is measured in a state in which the fuel cell vehicle is stopped before being started, reaches a reference temperature is derived. The required time required from a point in time at which the stopped vehicle coolant temperature is measured to a point in time at which the fuel cell vehicle enters the cold start mode is derived. A target heating value is corrected according to a ration between the estimated time and the required time to derive a final target heating value. The heating value of the fuel cell stack is caused to reach the final target heating value.