A flow cytometer control system using FPGA is designed. The traditional flow cytometry control system is very large and complex, with dozens circuit boards, hundreds or even thousands of chips. With the advantages of FPGA’s high speed, multiSelectIO interface and abundant logic resources, the control system can be optimized to a simple circuit board, with no more than a dozen chips. The improvements increase the reliability of the whole system, up the system process speed to megahertz. In FPGA algorithm, many difficulty problems are solved easily, such as multichannel data synchronization, peak search, area integration, etc. The control system can achieve up to 8 channels A/D data synchronous acquisition, 16 channel D/A output, several digital I/O output. In the experiment, a variety of control operations are steady achieved, and the 8peak rainbow calibration particles is measured and displayed.