Use three-axis magnetic instrument to measure ground magnetic field, and compensate the magnetic disturbance of measurement point. For reduce compensation cost, based on tradition 12-heft parameter method, combine the feature of sensor installation error, put forward a new compensation method, use this method to carry out compensation test by adopting iron block to simulate carrier disturbance under real environment. The results show that this method effectively improves the magnetic measure accuracy, and the error is improved from -258 ~3 430 nT to ±91 nT.