Abstract: Evaluating community structure where those endangered plant species occur and their population regeneration are essential for planning protection strategies. Thuja sutchuenensis, a critically endangered species restricted to a single population on the southern side of the Dabashan Mountain, Chongqing, southwestern China, has received little attention so far. We conducted a field investigation into Th. sutchuenensis community on community structure, floristic composition, stratification structure, size structure population and the regeneration of Th. sutchuenensis to provide an effective reference and scientific basis for the protection and management of the remaining Th. sutchuenensis. 10 stands (size: 20 m×20 m) were selected for sampling after repeated reconnaissance based on the factors of altitude, site conditions and so forth. The results showed that the population of Th. sutchuenensis was isolated into several smaller populations because of the habitat fragmentation, and “island” pattern. The community had high level of biodiversity and species richness (182 species belonging to 156 genera and 75 families were found, most of which belonged to Rosaceae, Liliaceae, Compositae, Lauraceae, and Cornaceae families); Gleason, Simpson, Shannon-Wiener diversity and Pielou index were high in the tree layer and shrub layer. The Th. sutchuenensis was mainly distributed in the vertical structure of shrub, lower and middle layers except upper tree layer. There were serious obstacles to population regeneration of Th. sutchuenensis because of the discontinuous distribution of the diameter of individuals. Meanwhile, the remaining Th. sutchuenensis population development was in an unstable environment, and the succession of broadleaf trees led negative influences on the regeneration of Th. sutchuenensis. We conclude that obstacle to the population regeneration of Th. sutchuenensis might be caused by the invasion and development of broadleaf trees in the community. We suggest that increasing habitat connectivity and decreasing the invasion of broadleaf trees should be the priority for the effective protection of Th. sutchuenensis.