Low-altitude unmanned aerial vehicle (UAV) photogrammetry combined with structure-from-motion (SFM) algorithms is the latest technological approach to imaging 3D stereo constructions. At present, derivative products have been widely used in landslide monitoring, landscape evolution, glacier movement, volume measurement, and landscape change detection. However, there is still a lack of research into the accuracy of 3D data positioning based on the structure-from-motion of unmanned aerial vehicle (UAV-SFM) technology, itself, which can affect the measurable effectiveness of the results in further applications of this technological approach. In this paper, validation work was carried out for the DJI Phantom 4 RTK UAV, for earth observation data related to 3D positioning accuracy. First, a test plot with a relatively stable surface was selected for repeated flight imaging observations. Specifically, three repeated flights were performed on the test plot to obtain three sorties of images; the structure from motion and multi-view stereo (SFM-MVS) key technology was used to process and construct a 3D scene model, and based on this model the digital surface model (DSM) and digital orthophoto map (DOM) data of the same plot with repeated observations were obtained. In order to check the level of 3D measurement accuracy of the UAV technology itself, a window selection-based method was used to sample the point cloud set data from the three-sortie repeat observation 3D model. The DSM and DOM data obtained from three repeated flights over the surface invariant test plots were used to calculate the repeat observation 3D point errors, taking into account the general methodology of redundant observation error analysis for topographic surveys. At the same time, to further analyze the limits of the UAV measurement technique, possible under equivalent observation conditions with the same processing environment, a difference model (DOD) was constructed for the DSM data from three sorties, to deepen the overall characterization of the differences between the DSMs obtained from repeated observations. The results of the experimental study concluded that both the analysis of the 3D point set measurements based on window sampling and the accuracy evaluation using the difference model were generally able to achieve a centimeter level of planimetric accuracy and vertical accuracy. In addition, the accuracy of the surface-stabilized hardened ground was better, overall, than the accuracy of the non-hardened ground. The results of this paper not only probe the measurement limits of this type of UAV, but also provide a quantitative reference for the accurate control and setting of an acquisition scheme of the UAV-based SfM-MVS method for geomorphological data acquisition and 3D reconstruction.