Natural disasters occur frequently causing huge economic losses and reduced grain production. Therefore, it is important to thoroughly explore the spatial correlations between grain, disaster, and the economy. Based on inter-provincial panel data in China in 2019, this study integrates complex network and co-occurrence theory into a coupled grain–disaster–economy (GDE) multilayer network, which provides a new perspective to further explore the spatial correlation between these three systems. We identify the spatial coupled characteristics of the GDE multilayer network using three aspects: degree, centrality, and community detection. The research results show the following: (1) Provinces in the major grain-producing regions have a stronger role in allocating and controlling grain resources, and the correlation between grain and disasters in these provinces is stronger and more prone to disasters. Whereas provinces in the Beijing–Tianjin–Hebei economic zone, and the Yangtze River Delta and Pearl River Delta economic zones, such as Beijing, Tianjin, Jiangsu, Shanghai, and Zhejiang, have a high level of economic development, thereby a stronger ability to allocate economic resources. (2) The economic subsystem assumes a more important, central role compared with the grain and disaster subsystems in the formation and development of the coupled GDE multilayer network, with a stronger coordination for the co-development between the complex grain, disaster, and economy systems in the nodal provinces of the network. (3) The community modularity of the coupled GDE multilayer network is significantly higher than that of the three single-layer networks, indicating a more reasonable community division after coupling the three subsystems. The identification of the spatial characteristics of GDE using multilayer network analysis offers a new perspective on taking various measures to improve the joint sustainable development of grain, disaster, and the economy in different regions of China according to local conditions.