The single photon counting technique is an effective method for detecting weak optical signals by using a photomultiplier tube, which is widely used in lidar detection in the area of aviation.Considering that lidar echo signals have such characteristics as weak strength, large data volume and high real-time requirements, we designed a high-speed data acquisition system based on the FPGA chip.The system accurately detects the weak lidar echo signal by using the photomultiplier tube, and the counting collection without time intervals is realized through the ping-pong operation by using two photon counters.Storage controllers and transmission controllers are used to control the peripheral chips.In this way, the real-time caching and high-speed transmission of the acquired data are realized.In order to verify the effectiveness of the proposed system, it was applied to the mie-scattering micro-pluse lidar and realized an effective detection of 7.5 km with a detection accuracy of 7.5 m.On this basis, a comparison was made to the measurement results of the acquisition system and the EASY-MCS photon counter.The mean square error was 8%.It indicates that the proposed system has high accuracy and stability, and can meet the requirements of weak echo signal acquisition of the lidar, which will have broad application prospects in the field of aviation meteorological detection.