Qinling Mountain with abundant species resources, was considered as one of the most important biodiversity hotspots in China. In this research, 43 administrative counties in Qinling Mountain were chosen as the study areas. Based on distribution of protected plants on the county level, and the species distribution range obtained from the database on vertical distribution and habitat types of the wild plants, spatial distribution patterns of species richness and hotspots of plants under state protection were studied. The results showed that: (1) there are 200 state protected plants in Qinling Mountain, among which 20 species were under category Ⅰ and 180 species were under category Ⅱ; (2) the overall distribution pattern of species richness is a zonal distribution along the mountain decreasing from east to west of the mountain and unfolding with a broom shape between the mountains and basins in the east of Qinling Mountain. Furthermore, the species richness in the south slope is much higher than that in the north slope; (3) three hotspots were identified by the spatial distribution patterns of species richness, including Funiu-Xiong'er mountainous region, Taibai-Foping mountainous region and the southeastern mountainous region of Tianshui. The conservation gap can be identified by overlaying the hotpots and the distribution of national nature reserve. Results of this study would provide important basic information for the further scientific biodiversity protection in Qinling Area.