Urbanization provides both challenges and opportunities for biodiversity conservation, but patterns of urban plant diversity across land uses, especially in Asian countries, remains unclear. To determine these patterns of diversity, woody plants in 174 sample quadrats across various land use types in Kyoto City were investigated. Richness, abundance, and evenness were evaluated at city, land use, and quadrat scales, and biodiversity of different land use types was compared. At the city level, 223 species in 77 families were recorded. At the land use level, residential areas had the highest total biological richness, with moderate to low evenness, while commercial areas exhibited low richness. At the quadrat level, the low-rise residential area had higher species richness than the other land uses. Species abundance and evenness in quadrats were significantly different across land use types for the canopy layer but not for the understory. The results provide insights into urban biodiversity design and management by identifying prior land uses for biodiversity improvement and by highlighting the contribution of residential private yards. Urban heterogeneity, scale, and multidimensionality should be considered when measuring urban biodiversity.