The spaceborne micropulse photon-counting lidar can realize high repeat frequency and multi-beam detection for the ground targets, improve the sampling density and coverage width of lidar in-orbit measurement effectively, meet the high-efficiency and high-precision surveying and mapping requirement. The simulation model was established based on the multi-pixel photomultiplier tube (PMT) considering the working principle of micropulse photon-counting lidar. Then the typical detection process of the micropulse photon-counting lidar was analyzed. The results show that the increase of pixel of PMT can obviously decrease the first photon effect of the lidar, improve the ranging accuracy. The ranging standard deviation of lidar would increase obviously with the increase of terrain slop. In addition, the distribution characteristics of the terrain profile can be described more accurately by the photon-counting point cloud with the increased number of pixel and arriving photons. Meanwhile, the airborne flight test verifies that the numbers of effective echo photons points increase obviously with the increasing pixel of PMT, which can reflect the contour features of tested terrain more accurately and efficiently. It can realize the high-precision photon-counting ranging under the complicated terrain, verify the correction of the simulation analysis result.