The characteristic protection villages (CPVs) are the basic types of rural revitalization, and one of the essential carriers of rural cultural heritage. Identifying its spatial structure characteristics contributes to the inheritance and continuation of rural civilization. Based on the CPVs data in Hubei Province, this paper identified spatial structure and evolution characteristic of CPVs in the perspective of spatial distribution types, direction, density, and equilibrium, respectively. At the same time, the Geodetector was used to analyze the influence mechanism of CPVs from 2009 to 2020. The main results showed that: (1) The spatial distribution of CPVs was an agglomeration structure type, which showed an increasing agglomeration trend of evolution characteristics in Hubei Province. And among them, the traditional villages (TVs) had the highest degree of agglomeration. (2) The CPVs showed the pattern of “east (slightly south) – west (slightly north)” with strong centripetal force and obvious directional, and they also showed a trend of gradual diffusion to east and west. (3) The high–density areas of CPVs presented an evolution trend from scattered independent structure to massive cluster structure, and generally presented a horizontal V shape kernel density structure. Meanwhile, the high–density areas of different types of CPVs had significant differences. (4) The CPVs were distributed in an unequal probability, and there were agglomerations in Yichang, Jingzhou, Shiyan, Xiangyang, and Enshi where it showed a gradually balanced development trend. The natural environment is the background and cornerstone of the site selection and layout of CPVs in Hubei Province. The influence of resource endowment, social economy and policy environment on the spatial distribution of CPVs are increasing gradually, and there are significant differences between different types of CPVs affected by various factors. We try to fill the gap in quantitative identification on the structure of CPVs to enrich the research regarding the special type features mechanism, which has significance for the protection and revitalization development of CPVs.