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In order to meet the demand of high-speed and high-precision acquisition of weak signal acquisition by flow cytometer, a multi-channel high-speed and high-precision data acquisition system based on FPGA and STM32 control is designed. The system receives and modulates the microvolt-level cell pulse electrical signal after amplification and photoelectric conversion, and transmits it to the FPGA for identification by analog-to-digital conversion, and then reads and transmits it to the upper computer for analysis and processing by STM32. FPGA combined with STM32 MCU is used to control its peripheral chips, it realizes synchronous data acquisition, real-time buffering and high-speed transmission. In order to verify the effectiveness of the system, it was tested by rainbow eight-peak microspheres. The experimental results showed that the detection limit of the fluorescence channel and fluorescence linearity were in line with national standards and met the high precision requirements of flow cytometry data acquisition, which means it has a broad application prospect in the field of medical electronic instrument design.