1. Anthropogenic environmental changes are known to affect the Earth’s ecosystems. However, how these changes influence assembly trajectories of the impacted communities remains a largely open question. 2. In this study, we investigated the effect of elevated nitrogen (N) deposition and increased precipitation on plant taxonomic and phylogenetic β-diversity in a 9-year field experiment in the temperate semi-arid steppe of Inner Mongolia, China. 3. We found that both N and water addition significantly increased taxonomic β-diversity, whereas N, not water, addition significantly increased phylogenetic β-diversity. After the differences in local species diversity were controlled using null models, the standard effect size of taxonomic β-diversity still increased with both N and water addition, while water, not N, addition, significantly reduced the standard effect size of phylogenetic β-diversity. The increased phylogenetic convergence observed in the water addition treatment was associated with the colonization of different, but phylogenetically closely related, species into different replicate plots of the treatment. Species colonization in this treatment was found to be trait-based, with leaf nitrogen concentration being the key functional trait. 4. Synthesis. Our analyses demonstrate that anthropogenic environmental changes may affect the assembly trajectories of plant communities at both taxonomic and phylogenetic scales. Our results also suggest that while stochastic processes may cause communities to diverge in species composition, deterministic process could still drive communities to converge in phylogenetic community structure.