Urban habitat gardens, designed at the urban community scale, are increasingly recognized as vital components of urban green infrastructure, contributing to biodiversity conservation and enhancing urban resident well-being. Despite their growing implementation, comprehensive studies examining their delivery of cultural ecosystem services (CESs) in densely populated areas remain limited. Previous research has predominantly focused on ecological impacts while largely neglecting the social dimensions influencing CES perception and valuation. This study bridges this gap by conceptualizing the multiscale feedback framework linking cultural ecosystem services and urban socio-ecological drivers. Using a mixed-methods approach, we then testified the conceptual framework by a case study focusing on eight habitat gardens in Changning District, Shanghai city of China. Results indicate that recreational and aesthetic values were most highly rated, while inspiration received the lowest valuation. Approximately 30% of residents reported disservices including animal disturbances, safety concerns, and health issues. Both social factors (age, education, gender, employment), usage patterns (visit frequency, duration), and ecological characteristics (plant diversity, landscape connectivity) significantly influenced CES perceptions. The findings underscore the necessity of integrating ecological properties with community characteristics to optimize habitat gardens’ efficacy in biodiversity conservation and CES delivery. We recommend holistic strategies that balance ecological and social sustainability in urban planning.