As the data acquisition component of lidar, single photon counter is designed to achieve the PMT output pulse signal count, and real-time upload the data to the computer. Because the rise time of the pulse signal is very short and the volume of data is very large, using CPLD as the counter and controller, using gated dual channel seamless counting method, the system can achieve 50 ns gate width resolution. Using a piece of 32 K×16 bit SRAM as cache can meet the requirements of maximum counts of 65535 per 50 ns time resolution. Using the USB as data transmission interface can meet the design requirements of high speed and real-time very well.