Achieving the coordinated development of the logistics industry, new urbanization and the ecological environment is significant for improving the efficiency of the logistics industry, urbanization level and environmental quality, but there are few studies that consider all three together. Based on the panel data of 11 provinces and municipalities in the Yangtze River Economic Belt from 2009 to 2019, this paper constructs the evaluation index system of the logistics industry, new urbanization and the ecological environment. The entropy method, coupled coordination degree model and exploratory spatial data analysis method are used to empirically analyze the spatial and temporal evolution patterns of the coupled coordination of the three systems in the Yangtze River Economic Belt. The results show that: (1) during the study period, the comprehensive development level of each subsystem and composite system in the Yangtze River Economic Belt has been improving, but there are some differences in the development among the systems in each region; (2) the coupling coordination degree of the three shows a smooth upward trend and an overall transition from near incoordination or basic coordination to the level of primary coordination or intermediate coordination, showing a spatial distribution pattern of downstream > midstream > upstream; (3) the spatial agglomeration characteristics show significant positive spatial correlation and agglomeration and are dominated by high–high agglomeration and low–low agglomeration. These reflect the enormous spatial and temporal differences in the coupling coordination of the three systems in the Yangtze River Economic Belt. The study takes the perspective of the coupled and coordinated development of the logistics industry, new urbanization and the ecological environment, which can provide references for enterprises and governments to make sustainable industrial and urbanization development strategies.