Single photon laser height measurement has become a trend in the field of laser altimetry. Referring to the data processing algorithms of laser point clouds at home and abroad and the accurate analysis of the characteristics of the single photon laser data with the high repetition rate and profile along the track, a single photon laser data processing method based on Terrain Correlation and least square curve fitting was proposed. The experiment using the photon cloud data obtained by NASA′s airborne Lidar—MABEL(Multiple Altimeter Beam Experimental LiDAR) was implemented, and the accuracy was validated by the simulated data. The results show that the method can effectively eliminate noise, and the overall precision can reach to 97.8% in the experimental region.