For the miniaturization of two-dimensional autocollimator, a method of using embedded measurement system instead of special host computer is presented. This system integrates CMOS image sensor's driving circuit, frame processing, adaptive exposure control, centroid subdivision and localization of cross, misalignment angle calculation, display driver and other functions within a FPGA chip, and the sampling image and measurement results are displayed through the TFT-LCD mounted on the device body. The engineering prototype shows that the system has characters of high precision, high integration and high reliability.