The loss of system precision owing to machining and installation errors is common in the assembly of micro magnetic parts. To overcome this issue， an automatic calibration and error compensation method is proposed herein. The coordinate systems of different modules are established according to the equipment layout， and all the error parameters affecting the assembly accuracy are extracted. According to the positional relationship of the guide rails， a model for motion transformation between different modules is established， and an error compensation model is then derived to meet the assembly task. The machine vision system in the equipment is used to take measurements， and a special calibration board is designed. The error parameters are measured and identified by observing the coordinate changes in the feature points before and after motion. Furthermore， all parameters are globally optimized via particle swarm optimization. Based on the developed automatic calibration software， calibration and verification experiments are carried out in the assembly operation area. The experimental results show that the open-loop control accuracy of the system is within 6 μm after compensation， meeting the assembly accuracy requirements of the equipment. This method provides an automated， high-precision and high-efficiency calibration scheme for the assembly equipment of micro parts.