Photon counting detection has extremely high detection sensitivity and has become the mainstream detection method of atmospheric detection Lidar. This paper designs an 8-channel high-count rate photon counting system based on FPGA. It is proposed a pulse detection method based on multi-phase clock over-sampling. The system can achieve the photon pulse width resolution of 2 ns, photon counting rate of 200 MCPS, and continuous multi-channel synchronous counting without dead time. It has the advantages of high counting rate, high real-time performance and high integration. The system is now equipped in the atmospheric multi-wavelength Raman polarization Lidar (AMPLE) developed by Beijing Research Institute for Telemetry(BRIT), which plays an important role in Lidar atmospheric remote sensing.