A fuel supply system of a vehicle, may include a fuel tank storing ethanol therein, a main injector installed at an engine to inject the ethanol from the fuel tank, a heater provided to heat the ethanol supplied from the fuel tank to the engine, a cold-starting injector installed at the engine to inject the ethanol heated by the heater, and a valve unit connected to the main injector and the cold-starting injector and performing a switching operation between a state of the ethanol being supplied from the fuel tank to the main injector and a state of the ethanol heated by the heater being supplied to the cold-starting injector.