<p>Urbanization constitutes a primary driver of the global biodiversity crisis, yet how historical urban legacy effects shape contemporary biodiversity remains unclear. Neglecting lagged ecological consequences such as extinction debts and colonization credits could obscure both the risks of future urban biodiversity loss and the effectiveness of conservation efforts. Here, by integrating equilibrium and non-equilibrium models, we quantified 31-year legacy effects of urbanization on bird communities and species in China. We found that China’s uneven urbanization has generated widespread extinction debts and colonization credits across the taxonomic, functional and phylogenetic dimensions of bird communities. The lag durations of various urban environmental characteristics differed, with historical vegetation cover and anthropogenic activities having long-lasting impacts on existing bird distributions. In particular, species-specific lagged responses were identified, which were correlated with each species’ capacity to adapt to urban environment (urban tolerance). These findings underscore the necessity of integrating long-term biodiversity considerations into urban governance through forward-looking approaches as well as providing critical insights for biodiversity-friendly urban planning.</p>