Aims Quantifying the relative importance of the mechanisms that drive community assembly in forests is a crucial issue in community ecology. The present study aims to understand the ways in which niche-based and spatially based processes influence community assembly in areas in different climatic conditions and how these processes change during the transition from seedling to adult. Methods In this study, we investigated how taxonomic and phylogenetic beta diversity in seedling and adult stages of forest trees change across three elevational transects in tropical, subtropical and subalpine forests in Southwest China, and the relationships of these changes to the environment and inter-site distances. We quantified the relative contribution of environmental conditions and spatial distribution to taxonomic and phylogenetic beta diversity of both seedling and adult life stages along each elevational transect. We also quantified the taxonomic and phylogenetic similarity between seedlings and adult trees along elevations. Important Findings Taxonomic and phylogenetic beta diversity of both seedlings and adult trees increased with an increase in both environmental distance and spatial distance in all three transects. On both taxonomic and phylogenetic levels, the effects of environmental filtering and spatial disposition varied between life stages and among forest types. Phylogenetic similarity between seedlings and adult trees increased with elevation, although the taxonomic similarity did not show clear elevational patterns. Our results suggest that the relative contribution of niche-based and space-based processes to taxonomic and phylogenetic assemblages varies across major plant life stages and among forest types. Our findings also highlight the importance of ontogenetic stages for fully understanding community assembly of long-lived tree species.