In order to promote the sustainable and coordinated development of the logistics industry and the manufacturing industry in the Yangtze River Economic Belt of China and provide the policy makers with decision-making references, this paper explored the spatio-temporal evolution of the coupling coordination development level of the two industries. A three-stage super-efficiency SBM model, which eliminated the influence of environmental factors and random errors, was constructed to make it possible to conduct an in-depth comparative analysis on the effective decision-making units (DMUs), making the calculation results more accurate. This was the main contribution of this paper. Based on the new model considering undesirable output, this paper analyzed the panel data of 11 provinces and cities in the Yangtze River Economic Belt from 2007 to 2017 and investigated the coordination development level from the dimensions of time and space considering the energy input and carbon emissions of the two industries. Our main research findings were as follows. First, due to the relative lagging of the logistics industry in promoting the development of the manufacturing industry, the overall level of the coordination between the two industries was at a stage of limited coordination. Second, the regional differences were significant with a spatial evolution pattern of “high in the east and low in the west”. Third, environmental factors affected the input efficiency of the logistics industry and the manufacturing industry, especially the latter. Overall, this paper made theoretical and practical contributions to promoting the joint development of the two industries, improving the logistics industry and upgrading the manufacturing industry.