A system and method of controlling a shift mechanism for a vehicle, includes a shift determination unit configured to determine information on a shifting stage of the vehicle according to an operation of the shift mechanism; and a control unit configured to receive the information on the shifting stage from the shift determination unit and to transmit a signal such that vibration is generated in the shift mechanism when the shifting stage switched by operation of the shift mechanism is a drivable shifting stage, wherein when a driver operates the shift mechanism to switch a shifting stage to a drivable shifting stage, a signal according to the corresponding shifting stage is transmitted to enable the driver to recognize the switched shifting stage and thus to prevent erroneous operation, ensuring driving safety.