The promotion of transportation system construction of Yangtze River economic belt to bring the basic and leading role of the transportation system construction into fully play is of important significance to implement the national strategy of Yangtze River economic belt. Based on the background, strategic significance and spatial layout of Yangtze River economic belt as well as spatial pattern of Chinese logistics evolution, this paper discusses the status quo, problems, plan goal and construction focus in comprehensive three-dimensional transportation system of Yangtze River economic belt, empirically analyzes the integration of Chongqing strategy and the transportation system construction of Yangtze River economic belt and provides the reference for Yangtze River economic belt construction.