Sub-alpine coniferous forest ecosystems are sensitive to climate change. However, the community formation mechanisms of sub-alpine coniferous forests in northeastern Asia remain poorly understood. In this study, we assessed the factors controlling the phylogenetic community structure in different strata (whole strata, upperstory, and understory) of Abies nephrolepis and Abies koreana forests in the sub-alpine zone in South Korea. Piecewise structural equation modeling (pSEM) was performed based on terrain, climate, taxonomic diversity, stand structure characteristics, and disturbance factors. The controlling factors presented different responses for each species depending on the stratum and phylogenetic community structure indices (net relatedness index and nearest taxon index). A. nephrolepis showed a unique community formation mechanism and formed climate refugia through high rock exposure, whereas A. koreana showed niche conservation at high elevations and a community overdispersion trend when forest gaps appeared due to overstory vegetation loss. The Mantel test and partial Mantel test were performed to examine the impact of turnover and nestedness on phylogenetic β-diversity, as well as to establish their correlations with climatic, geographic, and environmental distance. Turnover was a major contributing factor to β–diversity and strongly correlated with environmental distance. Further, geographical and climatic distance presented differential contributions to each species depending on the community characteristics. Integrated analyses of phylogenetic community structure and β-diversity provided detailed insights into the mechanisms underlying community formation and biodiversity patterns. This reveals that biodiversity patterns are driven by interactions between community structure and inter-community characteristics, with internal structure as a key mechanism influencing β-diversity.