A system control method is provided for measuring a distance between a smart key and a vehicle. When the distance between the smart key and the vehicle is changed based on a predetermined distance whether a hydrogen leak occurs is detected by a hydrogen sensor detection controller. A driver is then informed of a hydrogen leak via a display on a cluster, a turn-on of an emergency light, and a warning sound of the vehicle. Alternatively, a starting-impossible state of the vehicle or shutting-down starting of the vehicle is maintained to ensure safety measures based on the concentration of the leaking hydrogen.