Purpose A new in-vacuum three-dimensional Hall probe magnetic measurement system is under fabrication for characterizing the magnetic performance of the Cryogenic Permanent Magnet Undulator (CPMU). In order to fit the small gap (5 mm) of magnetic structure and vacuum environment, a small three-dimensional Hall probe has been manufactured. The angular and positional misalignment errors of the Hall sensors play an important role in the measurement accuracy of the CPMU. In order to minimize the misalignment errors, a method of calibrating angle error and relative assembly displacements of a three-dimensional Hall probe is carried out. Methods The angle error of Hall sensors will be calibrated by a standard dipole magnet and a five-dimensional Hall bench. The standard dipole magnet will generate a single direction and uniform magnetic field. And the fivedimensional Hall bench is used to rotate the Hall probe which is put in the center of magnet. Based on the relationship between angle and magnetic field strength, the angle error of each Hall sensor will be obtained. The relative position between the sensitive areas of the Hall sensors will be