Port logistics, which is a special form of integrated logistics system, gradually develops through the long-term interactions of natural, social, and economic factors. The strong spatial agglomeration and organizational capacity of port logistics on global supply chain elements (such as material flow, business flow, information flow, and capital flow), makes it a critical factor influencing regional survival, competition, and development. Thus, the formation and evolution of port logistics has become a topic of research interest in the transportation geography sector. Based on the connotation of port logistics, this study takes the major 22 ports along the Yangtze River as the research object and develops a comprehensive evaluation index system of port logistics development. This study then analyzes the spatio-temporal evolution characteristics and mechanism of port logistics development along the Yangtze River, by using the methods of Gini coefficient and standard deviational ellipse. Our study revealed that: (1) The development of the port logistics system along the Yangtze River has significant zonal differences. The overall development level of port logistics of the eastern, central, and western port groups is decreasing from east to west, but the growth rate is increasing from east to west. At the port level, a relatively large gap is observed in the comprehensive development level of port logistics along the Yangtze River due to the geographical environment, hinterland, transportation conditions, as well as other factors. Furthermore, we also found that the hierarchical structure characteristics of the port logistics system are evident. (2) With the constant development of the port logistics industry along the Yangtze River, development differences among the port logistics system and its three subsystems are constantly decreasing. Moreover, the effect sequence of the three subsystems on the comprehensive Gini coefficient of the port logistics system is as follows: city support, infrastructure, and logistics operation subsystem. (3) From 2004 to 2014, the gravity of the port logistics system has significantly transferred toward the upper and middle reaches of the Yangtze River. In addition, the major axes, minor axes, and area of the standard deviational ellipse of the port logistics system continued to grow. This indicates that there is an obvious decentralized tendency in the spatial pattern of port logistics development along the Yangtze River. (4) Lastly, this paper argues that the four main influencing factors of the spatio-temporal evolution of port logistics along the Yangtze River can be attributed to the balanced development of the regional economy, continuous optimization of the transportation network, intense hinterland competition among ports, and constant deepening of the regional port logistics cooperation.