Abstract: Thuja koraiensis, an endemic tree species in the Changbai Mountain, is listed as the China’s national second-level protected plant species. In this study, we investigated the habitat conditions and morphological indices of the naturally distributed T. koraiensis population in Changbai Mountain, to analyze its clonal population characteristics. We used grey relational analysis and path analysis to examine the relationship between population modules and soil factors based on the module theory. The results showed that: (1) The clonal population of T. koraiensis had strong phenotypic plasticity. The clonal population with patches distributed under dark coniferous forests had longer spacer length, larger aboveground expansion domain, higher ramet spacing than the population in T. koraiensis pure forest. The population modules had higher variability. (2) The clonal growth pattern of T. koraiensis was between intensive and guerrilla type. It had rapid clonal expansion ability and obvious patch distribution. In the pure forest community with nutrientpoor soil, the clonal growth pattern was closer to the intensive distribution. Under the dark coniferous forest with better soil conditions, the clonal growth pattern tended to be guerrilla distribution. (3) The response of T. koraiensis clonal population growth to soil heterogeneity was specific. Soil moisture was the most important factor affecting the expansion of T. koraiensis population. Soil pH, soil humic acid, soil available phosphorus, and soil available potassium were important factors affecting the clonal population modules of T. koraiensis. (4) Soil nutrients directly affected the characteristics of clonal modules and ecological adaptation strategies. The soil nutrients affecting each clonal module were in order of soil available phosphorus > soil available potassium > soil organic matter > soil total nitrogen.