A fuel injection system of a gas turbine includes a first pilot nozzle injecting fuel in a first flow rate range, a second pilot nozzle injecting fuel in a second flow rate range that is greater than the first flow rate range, a main nozzle injecting fuel in a third flow rate range that is greater than the second flow rate range, a first valve opening or closing a first supply pipe fueling the second pilot nozzle, a second valve opening or closing a second supply pipe fueling the main nozzle, and a controller selectively opening any one of the first supply pipe and the second supply pipe or opening or closing both of the first supply pipe and the second supply pipe by reflecting a change in altitude and thus applying control signals to the first valve and the second valve.