A macro-pulse photon counting Lidar is described in this paper, which was designed to implement long-range and high-speed moving target detection. The ToF extraction method for the macro-pulse photon counting Lidar system is proposed. The performance of the macro pulse method and the traditional pulse accumulation method were compared in theory and simulation experiments. The results showed that the performance of the macro-pulse method was obviously better than that of the pulse accumulation method. At the same time, a laboratory verification platform for long range and high-speed moving targets was built. The experimental results were highly consistent with the theoretical and simulation results. This proved that the macro pulse photon counting Lidar is an effective method to measure long range high-speed moving targets.