Abstract: In order to meet the needs of the automatic control of the newly developed 400 kV small heavy nuclide accelerator mass spectrometer (AMS) facility of China Institute of Atomic Energy, an automatic control system for the facility was designed and implemented. The article describes the system structure from two aspects of hardware and software, virtual instrument LabWindows/CVI9.0, PLC, database, configuration software, etc., to form a friendly human-computer interaction interface, and improve the reliability of the system. Self-designed gas stripper control with high automation level realizes synchronous monitoring, control of gas flow and vacuum. The combination of the zero indication and target number display of the automatic target change control achieves the target change function more accurately and improves the degree of facility automation. After a long time test, the measurement and control system realize the automatic control and local operation requirements of the accelerator mass spectrometry system.