Thuja sutchuenensis, a critically endangered gymnosperms restricted to a single population on the southern side of the Daba Shan (Chongqing, China), has received little attention so far. Based on investigation of many times, we used the floristic analysis, clustering analysis, heat analysis method and so on to studied floristic composition, community structure and collocation model of T. sutchuenensis community. The results showed that: (1) The community had high level of associated species richness and the life form of associated species is dominant of Nanophanerophyte, Hemicryptophyte, Microphanerophyte. Areal types are complex and temperate elements are more in the community. (2) The result of cluster analysis in the different sample plots showed that the altitude and spatial location were the important factors for influence the composition of the flora in the community. (3) When the community is dominated by shrub layer and lower tree layer, the number of individuals of T. sutchuenensis was more. We think that the average height of the community is the shorter, the better for expansion and regeneration of T. sutchuenensis populations. (4) According to the result of heatmap, we found that the following several patterns of the most conducive to the survival of the population of T. sutchuenensis which the T. sutchuenensis+Cyclobalanopsis multinervis+Carpinus fargesiana, T. sutchuenensis+Lithocarpus fangii+Cyclobalanopsis myrsinifolia and T. sutchuenensis+Pinus massoniana+Quercus semicarpifolia in the tree layer, and the T. sutchuenensis+Viburnum propinquum+Berberis julianae, T. sutchuenensis+Cotinus coggygria in the shrub layer. (5) T. sutchuenensis populations affected by high level of biodiversity and the higher associated species, so that it is particularly important to build a suitable model for the expansion and regeneration of the T. sutchuenensis populations by combined with the vertical structure of the community.