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To improve accuracy of parameters extraction of pulse signal, and accurately characterize a variety of physical and biochemical characteristics of cells, a data acquisition and processing system of fast pulse based on FPGA is designed. Firstly, the method of setting threshold value for both time window and amplitude is adopted to effectively avoid the noise influence during effective pulse recognition. Then, data collection, fast digital filter are realized, as well as pulse peak, area and width are extracted in parallel. An external host controller is constructed by using FPGA modules to control the internal FIFO of the USB chip CY7C68013A for achieving high speed data transmission. Finally, related experiments are implemented to verify the feasibility and system accuracy. Experimental results illustrate that real-time processing of pulse signal can be finished effectively and the data transmission speed of USB can be up to 29.8 Mb/s. 