Chemiluminescence immunoassay (CLIA) is the combination of chemiluminescence system and immunoassay. CLIA is established as one of the best alternatives to conventional radioimmunoassay for the quantitation of low concentrations of analytes in complex samples. A high-performance CLIA control system based on the embedded microprocessor S3C2410A is presented in this paper. The system principle, the overall structure of the system, the control structure of the key functional blocks and the flow chart of the software are given. The hardware drivers and the application software are developed on the basis of S3C2410A. The experimental results show that the presented system is feasible in the clinical diagnosis and can be used in the automatic chemiluminescence immunoassay analyzer.