Underground lava tubes are promising candidates for the construction of lunar bases because they are believed to offer good protection against radiation and harsh thermal environments on the lunar surface. Although the extent and structures of the underground lava tubes are uncertain, previously identified “skylights”, believed to represent places where lava tube roofs have collapsed, may provide insights into tube structures. Unfortunately, owing to the steep slopes, considerable depth, and associated difficult illumination conditions, the availability of detailed morphologic models of these pits is limited. In this study, we reconstruct the topography of lava tube pits using a refined photogrammetric approach. We use improved census cost for disparity search, refined point cloud coarse‐to‐fine registration, and weighted fusion of point clouds from several matched stereo image pairs to obtain a high‐resolution topographic model. Experiments are conducted for two prominent skylights, that is, the Mare Tranquillitatis Pit and the Marius Hills Hole, to demonstrate the effectiveness of the proposed approach. Several LRO NAC image pairs are selected from images covering these two areas, and fused topographic models with a spatial resolution of 2 are generated. The quality of our generated topographic models is validated against terrain products provided by the LROC team. Compared to these previous models, our model is generated based on a much denser point cloud and provides better coverage and more details. Benefiting from the detailed three‐dimensional models, morphological analysis is carried out to investigate the geometric dimensions (e.g., depth, diameters, slopes) of the lava tube pits.