The design and implementation of the control system of an ARM9-based biochemical analyzer was introduced in detail. The S3C2440, an ARM9-based MCU, was the core of the control system. Precision regulator circuit of light of the analyzer was designed to stabilize the voltage supply of the light source. Closed-loop motor positioning control technology and freely programmable CPLD stepper motor sub-circuit technology were used to precisely position the grating. And flexible gain control technology based on digital potentiometers was employed to solve the problem of signal regulation. Such core technical problems was solved in succession, it thereby improves the instrument's performance and function and provides a number of inexpensive high-quality products for domestic small and medium sized hospitals especially rural hospitals and promoted the establishment of those hospitals in consequence.