Rapid urbanization poses significant and multifaceted challenges to urban ecological environments, as well as to the physical and mental health of urban residents. In this context, urban biodiversity emerges as a key component that not only enhances a city's resilience and adaptability to environmental changes but also contributes meaningfully to the psychological well-being and life satisfaction of its inhabitants. Despite growing scholarly interest in the health benefits of nature, the specific pathways and mechanisms through which biodiversity exerts influence on human well-being remain underexplored, particularly in high-density urban environments. This study, rooted in the theoretical framework of environmental psychology, investigates the relationship between residents’ perceived biodiversity and their subjective well-being in Beijing, the capital of China. Drawing on survey data collected from urban residents and employing Partial Least Squares Structural Equation Modeling (PLS-SEM), the research seeks to identify both direct and indirect effects, with particular attention to the mediating roles of nature relatedness and restorative perception. Several important insights are revealed from this study: (1) Both perceived biodiversity and subjective well-being are generally rated at moderate levels among Beijing residents, yet significant differences are observed among demographic groups and across biodiversity dimensions; (2) Perceived biodiversity has a statistically significant and positive impact on subjective well-being, with plant diversity and biodiversity-related activities (e.g., green spaces, ecological infrastructure) showing the strongest effects; (3) Nature relatedness (i.e., an individual's emotional and cognitive bond with the natural world) and restorative perception (i.e., the psychological recovery experienced in natural settings) are not only positively influenced by perceived biodiversity, but also significantly enhance subjective well-being; (4) Importantly, nature relatedness and restorative perception serve as partial and sequential mediators, forming a chain mediation pathway that explains how biodiversity perception translates into enhanced well-being. By clarifying these psychological and perceptual mechanisms, the study advances our understanding of how urban biodiversity contributes to residents’ well-being beyond mere ecological or aesthetic value. These results underscore the importance of integrating biodiversity considerations into urban planning and public health strategies. The study offers practical implications for municipal governments, urban designers, and public health practitioners, suggesting that promoting biodiversity—particularly in terms of visible vegetation, ecological infrastructure, and educational engagement—can be an effective approach to fostering a healthier and more resilient urban population. Overall, this study provides valuable empirical evidence supporting biodiversity conservation as a pathway to sustainable urban development and enhanced quality of life in the rapid urbanization process.