A method of controlling a transmission of a vehicle may include beginning synchronization between a speed shift gear of a target gear and an output shaft to shift gears from a current gear to a lower gear set as the target gear in response to deceleration of the vehicle, after the synchronization between the output shaft and an input shaft by the speed shift gear of the target gear has been completed, maintaining the synchronized state therebetween for a predetermined time period, and completing engagement with the target gear to complete the shifting of the gears after the maintaining of the synchronized state.