On-orbit calibration technique is a key factor which affects the photon geolocation accuracy of spaceborne LiDAR. The current status of spaceborne LiDAR on-orbit calibration technique was introduced, and the characteristics of various spaceborne LiDAR on-orbit calibration technique were analyzed. Aiming at the characteristics of the photon counting mode spaceborne LiDAR, a new on-orbit calibration method based on the natural surface was derived, simulated point cloud was used to verify the correctness of the calibration algorithm, and a cross validation experiment was made with the surface data of the Antarctic McMudro Dry Valleys and China Lianyungang areas and ICESat-2 point cloud data, the experimental results show that the plane offset between the point cloud calibrated by proposed algorithm and point cloud provided by National Aeronautics and Space Administration is about 3 m, elevation offset is in centimeter scale. The differences between the point cloud calibrated by the algorithm and the point cloud provided by National Aeronautics and Space Administration were also compared by using the feature points of artificial construction on the ground. Finally, the accuracy of the on-orbit calibration method based on natural surface and the influence of the calibration field topography were discussed.