1. Anthropogenic environmental changes, such as nitrogen (N) enrichment and alteration in precipitation regimes, significantly influence ecosystems worldwide. However, we know little about whether and how these changes alter the phylogenetic properties of ecological communities. 2. Based on a seven-year field experiment in the temperate semi-arid steppe of Inner Mongolia, China, we investigated the influence of increased N and precipitation on plant phylogenetic structure and phylogenetic patterns of species colonization and extinction. 3. Our study demonstrated that N and water addition influenced different aspects of plant community structure. Water addition increased plant species richness by preventing species extinction and facilitating species colonization, without altering community phylogenetic structure. By contrast, N addition did not alter species richness, but promoted the colonization of species distantly related to the residents, changing community phylogenetic structure from being neutral to overdispersion. We also found evidence for abundance-based extinction where rarer species were at greater risk of extinction, and functional-based species extinction where shorter-statured plants and shallower-rooted plants were at greater risk of extinction. 4. Synthesis. Our study provides the first experimental evidence that plant phylogenetic community structure responds differently to different aspects of global changes. Importantly, the colonization of non-resident species, rather than the extinction of resident species, contributed predominantly to changes in plant community phylogenetic structure in response to N amendment. Our findings highlight the importance of considering species phylogenetic relationships for a more complete understanding of anthropogenic influences on ecological communities.