The coupling coordination of the logistics industry and manufacturing industry conducive to the sustainable development of logistics and manufacturing and the stability of sustainable supply chain. The logistics and manufacturing industries are not only the basic industries that support social development, but also the industries with high carbon emissions. Firstly, this paper classifies the carbon emissions from the logistics industry and manufacturing industry as undesirable outputs, evaluates the ecological efficiency of the logistics industry (LEE) and manufacturing industry (MEE) in the Yangtze River Delta from 2006 to 2019 by using the unexpected slacks-based measure (SBM) model. Secondly, the coupling coordination method is used to analyze the coupling coordination scheduling of industrial ecological efficiency. Thirdly, the paper analyzes the spatial differences of the coupling coordination ecological efficiency between logistics industry and manufacturing industry (MLCC) by using the exploratory spatial data analysis method. Finally, the spatial econometric model is used to analyze the driving factors of the MLCC. The results show: The ecological efficiency of the manufacturing industry has steadily improved. The ecological efficiency of the logistics industry presents the rising trend in fluctuation. The level of the coupling coordination development between the logistics and manufacturing industries is high. The results of the spatial heterogeneity analysis show that the spatial differentiation of high-high agglomeration and low-low agglomeration is obvious. The spatial agglomeration characteristics are relatively stable, and the spatial diffusion effect is strong; In space, the MLCC shows a trend of developing from multiple agglomeration areas to one agglomeration area. The results of driving factor analysis show that foreign direct investment(FDI), government intervention(GI) and human capital(HP) have positive effects on the MLCC, while industrial structure(IS), environmental regulation(ER) and energy intensity(EI) have negative effects on the MLCC.