The cross-border and spillover characteristics of natural disasters make the demand for cross-regional joint prevention and control of natural disasters increasingly prominent. The inter-regional emergency management policy coordination system has become the key to reducing vertical coordination costs and balancing regional and local contradictions. However, existing research mostly focuses on the measurement of the results of inter-regional policy coordination, and pays little attention to how the inter-regional policy coordination system can achieve a balance between regional common action and local differentiated risk response. By constructing a collaborative analysis framework for “structure-function” cross-regional emergency management policy, this paper uses an LDA topic model, TF-IDF weight analysis, and social network analysis to analyze the collaborative structure of the regional natural disaster policy coordination system in the Yangtze River Delta. Combined with the case of the Yangtze River Delta’s joint response to typhoon “MeiHua”, this paper analyzes the balanced role of the regional policy coordination system in promoting joint prevention and control of natural disasters. This paper finds that an effective inter-regional policy coordination system is a collaborative structure that can balance unified regional action with space for local adaptive response. In this structure, the policy objectives play a guiding role in strategic decision-making, balancing the regional requirements of joint prevention and control and the local demands of territorial risk response; policy tools play a complementary role in promoting emergency response capabilities, balancing regional collaborative standards and local tool preferences; the policy relationship plays the role of organizational relationship building, balancing the clear boundary of regional power and responsibility and the differentiation of local power, and the three jointly promote the coordinated development of cross-regional natural disaster joint prevention and control. The above findings reveal the transmission mechanism of the “structure-function” of cross-regional emergency management policy coordination, and provide practical paths and policy design principles for promoting the coordinated development of cross-regional emergency management.