University campuses are important components of cities, harboring the majority of urban biodiversity. In this study, based on monthly bird survey data covering 12 university campuses located either downtown or in the newly developed areas in Nanjing, China, in 2019, we studied the assembly processes of each campus’s bird population and their main drivers by modeling a set of ecological and landscape determinants. Our results showed that (1) bird abundance and species diversity in the newly developed areas were significantly higher than in those downtown; (2) the phylogeny of bird communities in all universities followed a pattern of aggregation, indicating that environmental filtering played a major role in community assembly; (3) specifically, grass, water, and buildings were the main factors affecting each campus’s bird community’s functional and phylogenetic diversity, with the areas of grass and water habitats having a significant positive correlation with phylogenetic diversity, while the size of building areas was negatively correlated. Our results emphasize that habitat features play a decisive role in determining urban bird population diversity and community assembly processes. We suggest that increasing landscape diversity, e.g., by reasonably arranging the location and area of water bodies and grasslands and improving the landscape connectivity, could be a powerful way to maintain and promote urban bird diversity.