The ICE, Cloud and land Elevation Satellite-2 (ICESat-2) can provide new measurements of the Earth's elevations through photon-counting technology. Most research has focused on extracting the ground and the canopy photons in vegetated areas. Yet the extraction of the ground photons from urban areas, where the vegetation is mixed with artificial constructions , has not been fully investigated. This article proposes a new method to estimate the ground surface elevations in urban areas. The ICESat-2 signal photons were detected by the improved Density-Based Spatial Clustering of Applications with Noise algorithm and the Advanced Topographic Laser Altimeter System algorithm. The Advanced Land Observing Satellite-1 PALSAR-derived digital surface model has been utilized to separate the terrain surface from the ICESat-2 data. A set of ground-truth data was used to evaluate the accuracy of these two methods, and the achieved accuracy was up to 2.7 cm, which makes our method effective and accurate in determining the ground elevation in urban scenes.