The coaxial software configurable optical test system (SCOTS) is an aspheric and freeform surface metrology method with high accuracy. The positioning accuracy of the test surface and screen seriously affects the measurement accuracy. In this paper, a novel method, PDCMC (positioning with differential computation, calibration board assisted, 3D measurement and component displacement), is proposed for the precise positioning in the coaxial SCOTS. In the proposed method, a flat crystal is used as the initial test mirror. In the initial system, the positioning of the screen is carried out using the differential computation method. Then, the positioning of a calibration board is carried out based on the feature points on the calibration board. The relative position and attitude among the flat crystal, the calibration board and the actual test surface are provided by a 3D coordinate measuring machine. Finally, through coordinate transformation and data processing, the precise positioning of the test surface and screen can be completed in the actual coaxial SCOTS. The proposed method is highly versatile and suitable for almost all kinds of test surfaces. Simulation and experiments demonstrate the feasibility and accuracy of the proposed method. Compared with the existing universal positioning method, the proposed method has the advantages of fewer required components and higher precision.