An imaging electronics system for a sunlight-induced chlorophyll fluorescence hyper-spectrometer has been designed to meet the detection requirements of high signal-to-noise ratio and high spectral resolution for weak fluorescence radiation. Based on the selection of complementary metal oxide semiconductor (CMOS), as well as the requirements of detection, the control module and the decoding module of communication protocol are developed, and then the design of CMOS imaging system is completed. The control part selects field programmable gate array (FPGA) with strong parallel data processing ability, and the communication selects Camera-Link protocol with fast communication speed and specially built for camera. The expected signal-to-noise ratio of the designed system is about 31 dB. The design of the imaging system provides a good solution for fluorescence detection system which requires low noise and high imaging quality.