The Qinghai-Tibet Plateau (QTP) is the highest and one of the most extensive plateaus in the world. Investigating naturalized non-native plant species composition, phylogenetic relationships among naturalized plant species, and phylogenetic relationships between native and naturalized plant species on the plateau is of great importance. Here, we analyze a comprehensive dataset including all species of native and naturalized vascular plants known to occur in the core part of the QTP. We use net relatedness index (NRI) and nearest taxon index (NTI), which reflect deep and shallow evolutionary histories, respectively, to quantify phylogenetic relatedness among angiosperm species. The QTP included in this study (1,448,815 km2) has 9086 and 314 species of native and naturalized non-native vascular plants, respectively. We find that the naturalized angiosperm species are phylogenetically clustered with respect to the species pool including all native and naturalized angiosperm species on the QTP included in this study, regardless of whether NRI or NTI is used. For the eight regions within the QTP included in this study, NRI and NTI of naturalized angiosperms are positive in seven regions with respect to their respective regional species pools, reflecting phylogenetic clustering. Thus, naturalized angiosperm species are a phylogenetically clustered subset of all angiosperm species on the QTP, regardless of whether the studied plateau as a whole or its constituent regions are considered.