Biodiversity and community assembly are central topics in ecological studies, and mountains present natural laboratories for studying these issues. Most previous studies have focused on biodiversity hotspots and tropical regions, and relevant research in the middle and high latitudes is relatively limited. We hypothesized that species dispersion and habitat filtering simultaneously might drive the assembly of the current plant community in temperate region mountains. We studied the plant community of the Kunlun Mountains, an independent physical geographic unit located in northwest China on the northern edge of the Qinghai-Tibetan Plateau. We integrated measures of species distribution, geological history, and phylogeography, and analyzed the taxonomic richness, phylogenetic diversity, and phylogenetic community structure of the current plant community in the area. The distribution patterns of 1,911 seed plants showed that species were distributed mainly in the eastern and the southeastern parts of the Kunlun Mountains, which were considered as conservation targets for biodiversity. Similarities of genera and species strongly indicated that mass species migrations exist among the Kunlun Mountains and adjacent biodiversity hotspots. This indicated that the current patterns of species diversity were from species recolonization, and the plant species of the Kunlun Mountains originated primarily from the Hengduan Mountains which are a biodiversity hotspot. The net relatedness index (NRI) indicated that 17 of the 28 communities were phylogenetic clustering, and the others were phylogenetic dispersion. The nearest taxon index (NTI) indicated that 27 of the 28 communities were phylogenetic clustering, and the phylogenetic community structure of Banma County was the only example of overdispersion. By combining the standard effect size phylogenetic diversity (SES-PD) with the two indexes, we showed that species recolonization was likely to be an important evolutionary process affecting the assembly of current plant communities, and that habitat filtering may have drove the ecological processes of these communities.