The construction of autonomous knowledge system of philosophy and social sciences with Chinese characteristics is the current theoretical research hotspot and discipline development focus. The discipline of emergency management has typical interdisciplinary characteristics. What logic should be used to construct the interdisciplinary autonomous knowledge system of emergency management with Chinese characteristics? What are the key elements and challenges of the build process? Based on the analysis of the current situation of the theoretical research and practical application of the interdisciplinary knowledge system of emergency management, this paper puts forward the construction logic of the interdisciplinary knowledge system of emergency management of "scenario response-knowledge integration", and holds that the construction process includes three key points: scenario orientation guides the direction of knowledge sources; Knowledge integration is the essential basis of knowledge structure; Fusion communication is the realistic demand of knowledge communication. Based on the exploration of the interdisciplinary textbook curriculum and teaching software development of emergency management by the team of Beihang University, this paper analyzes the challenges in the construction of the interdisciplinary knowledge system, such as disciplinary differences, knowledge background conflicts, lack of team cooperation mechanism, and lack of talent cultivation ability. At the same time, it puts forward prospects for the improvement of the China's autonomous interdisciplinary knowledge system of emergency management.