<p>Understanding the spatial distribution patterns and driving factors of phylogenetic diversity and structure in mountainous cities is crucial for biodiversity conservation. However, consensus on how these mechanisms operate has not yet been reached, particularly in subtropical mountainous cities. Therefore, this study takes Chongqing as an example, integrating Principal Coordinates of Neighbor Matrices, redundancy analysis, and hierarchical partitioning to systematically evaluate the relative contributions of topography, soil, climate, and anthropogenic disturbance to phylogenetic diversity and structure. The results showed that phylogenetic diversity increased significantly with elevation, exhibiting a distinct east-high-west-low pattern; phylogenetic terminal structure showed a trend of overdispersion with increasing elevation, and spatially presented a pattern of overdispersion in the central urban area and the Wuling Mountains, while clustering in surrounding regions. Topography was the primary driving factor, with slope shape, slope gradient, and aspect explaining most of the variation in phylogenetic diversity and structure. Soil factors had the second strongest influence, while climatic variables significantly affected only deep phylogenetic structure. Anthropogenic disturbance variables ranked second only to slope shape in influencing deep phylogenetic structure (SESMPD), but showed no significant effect on shallow phylogenetic structure (SESMNTD). The urbanization effect, modulated by topography, has reshaped the regional species pool around the central urban area. In conclusion, these findings further advance our understanding of vegetation diversity patterns and their formation mechanisms in mountainous cities. We recommend prioritizing the conservation of the Wuling Mountains, which harbors more ancient lineages, and call for urban planning that accounts for pre-existing topographical conditions.</p>