The study of industrial spatial linkages of urban agglomerations is crucial to recognizing spatial structure and optimizing regional division and cooperation. The existing studies often focus on external spatial interaction at the inter-city level, but few have considered complex internal economic linkages at the inter-sector level. In this study, we established an integrated framework by combining the wave effect gradient field with the gravity model. The wave effect gradient field was used to analyze the inter-sector relation, while the gravity model was adopted to explore the spatial interactions of industry at the inter-city level. The Urban Agglomeration in the Middle Reaches of the Yangtze River (UAMRYR) was taken as a case study, which demonstrates the applicability of the proposed framework. The results indicate that there exists an imbalanced development in the network of industrial linkages in the study region. Each subgroup has presented a self-organized spatial linkage network, but the linkages between subgroups are immature. Compared with other sectors, the high-tech and internet industrial sectors contribute most to economic linkages among cities. Thus, policymakers should take actions to strengthen the inter-subgroup spatial linkages and give priority to the high-tech industries, which is necessary for the integrated and sustainable development of UAMRYR.