<p>Maintaining the resilience and sustainability of social-ecological systems (SESs) is widely acknowledged as a pivotal governance objective. However, the tendency to analyze these aspects separately raises concerns regarding potential inherent trade-offs between them, wherein bolstering one may impede the other. Addressing this, we present a reconciled framework to elucidate the relationship between resilience and sustainability. Our framework highlights that the fundamental linkages between humans and nature, which involve the acquisition of resources from the natural environment and the discharge of waste resulting from human production activities, as well as the feedback mechanisms from the natural environment in response to human activities, are the primary determinants of SESs’ resilience and sustainability. Sustainability necessitates these linkages staying within environmental boundaries while meeting socio-economic goals, whereas resilience means that these links can resist disruption and recover swiftly if disrupted by internal or external factors. Using the Yellow River Basin in China as a case study, we demonstrate how our framework can analyze SES evolution and drivers. Overall, our analysis underscores the importance of circumventing the trade-off between resilience and sustainability while fostering synergies, which could yield critical insights for the refinement of governance approaches of SESs.</p>