The continuation and accumulation of the global economic downturn has brought uncertainty and instability to China’s economic growth, signaling that further expanding domestic demand and deepening supply-side structural reform to achieve a higher level of virtuous cycle of the national economy is an important move for China to promote rapid and high-quality economic development. It is important to further explore the comprehensive interaction between the productive services agglomeration and manufacturing productivity in the multidimensional linkage space, which is important to enhance the manufacturing productivity precisely with the logic of interaction between the two industries, so as to facilitate the realization of domestic economic cycle. Using the panel data of 108 cities in the Yangtze River Economic Zone from 2007 to 2020 as a sample, this study first refines the research framework of “how the productive services agglomeration affects the improvement of manufacturing productivity” by including the spatial mismatch index of the two industries, and then re-examines the interaction between the two industries from the perspective of the complex network linkage space. The results show that, firstly, there is a spatial mismatch between productive services and manufacturing industries in the Yangtze River Economic Zone, and the degree of mismatch is gradually increasing. Second, in the industrial dimension linkage space, the spatial mismatch between the two industries can constrain their effective interaction. Third, when expanding the economic dimensional linkage space into a complex network linkage space, the two industry interactions show significant positive spillover effects, and the spillover effects are significantly larger than the local effects. Fourth, in the complex network linkage space, the spillover effect of the interaction between the two industries has obvious industry heterogeneity. Specifically, only high-end productive services agglomeration plays a significant spillover effect. Fifth, the comparison reveals that the complex network linkage space can also indirectly promote the effective generation of two-industry interaction by weakening the negative effect of the spatial mismatch. Based on the findings, this study argues that deepening the integration of production service industry and manufacturing industry by digital empowerment, promoting the expansion of high-end productive services agglomeration by recruiting talents and wisdom, and promoting the orderly flow of production factors across sectors by optimizing the layout of two industries are effective policy tools to help improve the productivity of manufacturing industry.