In the face of increasingly severe global resource crises and climate anomalies, enhancing natural resource governance capabilities to safeguard national ecological and resource security holds significant importance. From the perspective of “crisis-response” dynamic analysis, this study explored how natural resource governance actors shape system resilience through adaptive governance when confronting complex endogenous crises, thereby establishing the capacity to flexibly address diverse governance dilemmas. The study concluded that three key factors enable adaptive governance to function effectively: the theoretical underpinnings of participatory governance, the institutional drivers of ecological civilization system development, and the adaptive characteristics inherent in governance practices. Systemic resilience against complex endogenous crises stems from internal organizational interactions within the system, including multi-level governance structures aligned with ecosystems, government-led multi-stakeholder networks, and iterative knowledge generation. The study concluded by examining national parks’ response strategies to endogenous crises as a case study, illustrating the concrete manifestations of adaptive governance. It further analyzed challenges in national natural resource governance from an adaptive governance perspective and proposes corresponding policy recommendations.