The developed short wavelength X-ray stress lossless analyzer designed independently by a group is an important scientific instrument used to analyze the inner information of material without damage.Based on the system components and controlling requirement of the instrument, the design principle of the main function modules of the controlling system was discussed including mainframe and data acquiring, the X-ray controlling process, the test-rig motion controlling, the precision control of the goniometer system, the long-distance connection and security protection. Especially, the designed precision goniometer system got the highest level in international market.Test confirms that the integration of the controlling functions fulfills the automation control requirements of higher precision, higher stability and modularization with economical device.