A cooling system of a vehicle having a fuel cell stack includes a pump for circulating a coolant in a coolant line passing through the fuel cell stack, a heater disposed on the coolant line for heating the coolant by electric power supplied by a drive motor of the vehicle, and a controller for operating the heater by a surplus electric power generated by the drive motor when a heat generation amount of the fuel cell stack is less than a first threshold value and a rotation speed of the pump is above a second threshold value, and for turning off the heater when the heat generation amount of the fuel cell stack is less than the first threshold value and the rotation speed of the pump is less than the second threshold value.