Based on panel data of logistics industry from 11 provinces and cities in the Yangtze River Economic Belt from 2006 to 2021, the DEA Malmquist model is used to calculate the efficiency and total factor productivity index of logistics industry in each province and city in the Yangtze River Economic Belt. Cluster analysis and spatial autocorrelation analysis methods are used to reveal the spatiotemporal evolution characteristics of logistics industry efficiency and total factor productivity. The results show that the comprehensive efficiency level of the logistics industry in the Yangtze River Economic Belt is 0.789, and the overall efficiency level is not high. It shows a U-shaped trend in time and a stepped distribution pattern of high in the east and low in the west in space; The average total factor productivity index is 0.891, with a significant annual decline. There is currently no “stepped” distribution pattern in space, and technological progress is a key factor affecting the efficiency of the logistics industry in the Yangtze River Economic Belt. In terms of spatial correlation, the Global Moran’s I index is significantly positive, and the logistics efficiency of provinces and cities in the Yangtze River Economic Belt shows a spatial positive correlation. Provinces and cities with similar logistics efficiency are clustered and distributed in space, but the coordinated development between regions is uneven. Finally, in order to promote the coordinated development of the logistics industry in the Yangtze River Economic Belt, it is proposed to formulate differentiated logistics strategies, improve the level of logistics interconnection and development in the “river land air sea” region, promote the construction of information and intelligence, strengthen the support of logistics technology innovation, and build a green logistics full chain.