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In order to satisfy the needs of signal demultiplexing, line-field synchronization and pixel value reconstruction in a high-frequency pulse time-division multiplexed dual-independent scanning detection two-photon microscopy imaging system, the acquisition and processing of high-speed data were studied; Based on LabVIEW FPGA, combined with finite state machine, FIFO cache and parallel pipeline technologies, a multifunctional acquisition and processing system was designed，which successfully achieved lossless demultiplexing of high-speed data and subsequent imaging data processing through precise timing control, and was able to correct image distortion caused by the nonlinear motion of the resonant galvanometer; after debugging, simulation and experimental testing, Under the system's single-channel sampling rate of 800MSPS and 200MHz FPGA processing clock, it can perform complex processing on the corresponding fluorescence signals from different locations generated by 160 MHz time-staggered laser pulses. Practical applications have shown that the system meets the needs of real-time imaging and provides solutions for related fields. The researchers provided useful references.