To improve the alignment accuracy of the magnet in high energy synchrotron radiation source, the magnetic center is used instead of the mechanical center to calibrate, the magnetic center position of the magnet is obtained by vibration wire or rotation wire technology, and the position of the wire is measured by capacitive sensor, so as to realize the association between the magnetic center and the collimation target. To achieve high precision measurement of wire position, it is necessary to calibrate capacitance sensor accurately. In this paper, a kind of capacitive sensor is introduced and its calibration method is studied, the data acquisition method of grid and data processing method of high order polynomial fitting are proposed, the sensor calibration platform is built and the corresponding calibration program is developed, and the automatic and high precision calibration of the sensor is realized. Analysis and comparison show that the calibrated capacitance sensor has achieved the displacement measurement accuracy of μm level, which provides a basis for high-precision collimation of magnets.