A method for preventing a relay attack of a smart key system for a vehicle according to the present invention accurately calculates a current spaced distance between an SMK unit and a fob key by using an RSSI included in a response signal and a current voltage level in a process of decoding the response signal when the fob key carried by a user receives a signal applied from the SMK unit installed in a vehicle and then transmits the response signal having at least two kinds of information to the SMK unit, and detects a challenge signal applied from the SMK unit installed in the vehicle and a noise signal included in the response signal, thereby enabling an operation of the vehicle only in a state where the carrier of the fob key secures a predetermined visual distance from the vehicle, and more definitely preventing a third party from breaking into the vehicle through RF bi-directional authentication.