Cliffs are essential refuges for endangered plants, but their inaccessibility and inadequate reliable survey methods make the assessment of the survival status of these plants difficult. We employed the drone-based Nap-of-the-Object Photography (NoOP) technique, which involves flying close to an object's surface to automatically capture high-precision images of the object surface, to investigate an endangered cliff plant, Clematis acerifolia, in North China. A drone (DJI M300 RTK) equipped with a visible-light mapping camera (DJI Zenmuse P1) was used for automated NoOP flights, enabling the collection and reconstruction of millimeter-level, high-precision three-dimensional (3D) models of the cliff plots. Across 12 cliffs, we identified and measured the precise coordinates and values of eight microtopographical and five morphological characteristic factors for 1444 C. acerifolia plants. The Ground sampling distance (GSD) of the high-precision 3D models reached 0.10 cm/pixel, and the mean value of the root mean squared error of the sampled positioning coordinates was 4.65 cm/pixel. Correlation and correspondence analyses were used for data analyses. The results indicated that the growth status of C. acerifolia was significantly influenced by a complex factor interaction, particularly plant altitude, crevice width, and crevice length. This method for cliff plant surveys using drone-based NoOP determines the parameters for such surveys and demonstrates the effectiveness and potential of this method for cliff plant investigations. The primary microtopographical factors affecting the growth and distribution status of C. acerifolia were identified, providing pointers for translocation conservation and propagation reintroduction of this endangered plant.