Craters on the lunar surface are the most direct method for the study of geological processes and are of great significance to the study of lunar evolution. In order to fill the research gap on small craters (diameter less than 3 m), we focus on the small craters around the moving path of the Yutu-2 lunar rover and carry out a 3D reconstruction and geometrical morphology analysis on them. First, a self-calibration model with multiple feature constraints is used to calibrate the navigation camera and obtain the internal and external parameters. Then, the sequence images with overlapping regions from neighboring stations are used to obtain the precise position of the rover through the bundle adjustment (BA) method. After that, a cross-scale cost aggregation for a stereo matching network is proposed to obtain a parallax map, which can further obtain 3D point clouds of the lunar surface. Finally, the indexes of the craters are extracted (diameter D, depth d, and depth–diameter ratio dr), and the different indicators are fitted and analyzed. The results suggest that CscaNet has an anomaly percentage value of 1.73% in the KITTI2015 dataset, and an EPE of 0.74 px in the SceneFlow dataset, both of which are superior to GC-Net, DispNet, and PSMnet, and have higher reconstruction accuracy. The correlation between D and d is high and exhibits a positive correlation, while the correlation between D and dr is low. The geometric morphology expressions of small craters fitted by using D and d are significantly different from the expressions proposed by other scholars for large craters. This study provides a priori knowledge for the subsequent Von Karmen crater survey mission in the SPA Basin.