Urban socio-ecological systems (USES) that couple natural elements with human activities are critical for understanding urban ecosystem services and managing ecosystems to meet the needs of growing and diverse urban populations and sustainable development goals. However, the complexity of USES research topics and the comprehensiveness of research methodologies have made it challenging to conduct research in this filed. The theoretical foundations, analytical frameworks, and research paradigms are not yet unified. There is an urgent need to systematically review existing research and explore the theoretical foundations, analytical frameworks, and the content of USES. This paper reviews the relevant theoretical foundations of USES, mainly involving complex adaptive systems theory, coupled human and nature systems, socio-ecological urbanism, and urban metabolism theory. Meanwhile, the paper summarizes the analysis framework of USES, which mainly includes the multi-level analysis framework of social-ecological systems, the human ecological system model, the conceptual framework of USES, the conceptual model of USES based on natural solutions, the framework of urban social-ecological-technological systems, and the framework of socio-economic-natural composite ecological systems. Finally, the paper proposes a framework for analyzing sustainability of USES from an integrated perspective of vulnerability, resilience, and adaptation. Vulnerability, resilience, and adaptation are core research themes in sustainability science. They play a crucial role in integrating social and ecological elements, analyzing the intricate processes and mechanisms of social system and ecosystem interactions, and guiding the management of USES towards sustainability. The paper also provides methods for conducting research on the vulnerability, resilience, and adaptation of urban socio-ecological systems. Constructing a vulnerability evaluation index system based on exposure, sensitivity, and coping capacity, and conducting vulnerability assessments are crucial components for identifying disturbances in USES, evaluating the condition of USES, and analyzing the characteristics of USES issues. Resilience not only helps diagnose the state of USES and assess their ability to cope with disturbances, but also provides a framework for understanding the complex processes of interactions and dynamic evolution mechanisms within USES. Based on the long-term state change of the system, exploring the key time points of the system state change (regime shift) and its driving factors, and then revealing the evolution law of the USES is the main research approach in the field of USES resilience. Adaptation refers to the adjustment and response of USES to external disturbances. Adaptive management of USES is essential for integrating urban ecological resources and planning management, mitigating the vulnerability of USES, and enhancing their resilience and sustainability. This study can offer valuable lessons and insights for the study of USES in China, particularly for developing a framework for analyzing USES.