It is difficult to distinguish the spaceborne single-photon laser echo signal mixed with the noise. A two-step method for denoising spaceborne single-photon data based on statistical histogram is proposed. In order to eliminate noisy photons in the spaceborne single-photon echo data, a small window histogram method along the track is used for coarse denoising, and then a distance square statistical histogram method is used for fine denoising. The echo photon data of the Advanced Topographic Laser Altimeter System(ATLAS) spaceborne single photon lidar under three typical conditions of strong and weak beam, day and night, flat ground and mountain are selected as experimental data. Combined with the official results of ATLAS and based on the confusion matrix, the de-noising accuracy is calculated. Experimental results show that the denoising accuracy of strong beam data is 98.86%, and that of weak beam data is 96.94%; the denoising accuracy of night data is 99.02%, and that of daytime data is 98.86%; the denoising accuracy of mountain data is 96.28%, and that of flat data is 96.94%. The results show that the proposed method is suitable for spaceborne single photon data denoising under above three typical conditions.