A method and a system for vehicle head direction compensation are disclosed. The method includes the following. A relative position between each of a plurality of sensors disposed on a vehicle and a plurality of base stations is obtained through the sensors and a relative coordinate system is established by a processor to obtain a vehicle head direction of the vehicle in the relative coordinate system and a deviation angle between an X-axis of the relative coordinate system and a true north azimuth. An angle compensation is performed by the processor on the vehicle head direction of the vehicle in the relative coordinate system based on the deviation angle.