The autonomous driving method using magnetic sensors recognizes the position by measuring magnetic fields in autonomous robots or vehicles after installing magnetic markers in a moving path. The Position estimate method using magnetic sensors has an advantage of being affected less by variation of driving environment such as oil, water and dust due to the use of magnetic field. It also has the advantages that we can use the magnet as an indicator and there is no consideration for power and communication environment. In this paper, we propose an efficient sensor system for an autonomous driving vehicle supplemented for existing disadvantage. In order to efficiently eliminate geomagnetism, we analyze the components of the horizontal and vertical magnetic field. We propose an algorithm for position estimation and geomagnetic elimination to ease analysis, and also propose an initialization method for sensor applied in the vehicle. We measured and analyzed the developed system in various environments, and we verify the advantages of proposed methods.