This paper uses the three-stage DEA method to eliminate the influence of environmental variables and random factors，measures the efficiency of 20 major ports on the Yangtze River trunk line in 2010，2013，2016 and 2020，and clarifies the temporal and spatial evolution characteristics of each port efficiency. The results show that：1）The environmental variables and random factors have a significant impact on port efficiency.2）The efficiency of the main ports of the Yangtze River trunk line is quite different. The downstream ports are generally more efficient，while the middle and upstream ports are less efficient. 3）Low scale efficiency is the main factor that leads to the failure of comprehensive efficiency to achieve DEA effectiveness. Most of the ports have insufficient investment in resources，fixed assets and capital or have unreasonable structures，and have not been able to effectively exert their scale effects. 4）Some ports have low technical efficiency，and management efficiency and information level need to be accelerated. It is necessary to optimize the resource allocation and improve the port efficiency according to the actual development of each port.