The magnetic sensor and the acceleration sensor used in the magnetic borehole inclinometer bring errors to the output of the sensors due to their own difference in characteristics and their production and assembly， resulting in the deviation in the calculation of the drift angle and azimuth of the inclinometer. Therefore， the twelve-position calibration method is adopted to correct the three axis zero position deviation， sensitivity error and installation error of the magnetic sensor and the acceleration sensor according to the geomagnetic component and gravitational acceleration in the vertical direction. The comparison experiment before and after correction shows that the mean square error of the drift angle of the inclinometer is reduced from 0.5° to 0.06°， the mean square error of the azimuth is reduced from 21.75° to 0.82°. It demonstrates that the correction method is effective and can meet the requirements of the engineering application of the inclinometer.