In order to solve the fluorescence excitation problem of high throughput dPCR gene chip, a fluorescence excitation measurement and control system was designed in this paper. According to the excitation spectrum characteristics of fluorescent dyes, high-power narrow-band LED is selected as the fluorescent excitation light source and controlled by STM32 microprocessor system. The fluorescence excitation system has three fluorescence excitation channels including FAM, HEX and ROX, and the excitation power of each LED channel can be adjusted respectively. The maximum output current of the system is 8 A, the maximum output power of the single channel is 3 W, and the adjustment accuracy is less than 1.0%. The system could complete the fluorescence excitation and collection of 9 600 microdroplets of dPCR gene chip at one time. The experimental results show that the system meets the requirements of design and application.