The evaluation of ports in the Yangtze River System is important to scientifically reflect the status quo of port efficiency, which contributes to further achieving the port efficient operation and to constructing the Yangtze River Economic Zones. The present researches about port efficiency neglected the technology gap of the ports. In order to make up this shortcoming, the metafrontier efficiency, group efficiency and metatechnology ratio (MTR) of 21 major inland ports in the main stems of the Yangtze River system during 2010~2012 are analyzed using Data Envelopment Analysis (DEA) and MetaFrontier production function. The empirical analysis result shows that with the maximum mean value of metafrontier efficiency being just 0.27, the efficiency of major inland ports in the Yangtze River System is at a low level, and the efficiency of each group still has a very big promotion space; that with the values of average group efficiency being 0.58, 0.67 and 0.27, technological level varies in each group and is affected by the development of economy and geographic locations; that while MTR of Group Three is 1, it is up to the potentially best technology level but inefficiency of management is universal, and technology level and management efficiency of both Groups One and Two need to be enhanced, but the first thing for both is to continue to promote technology level. Furthermore, the Data Envelopment Analysis projection shows that the phenomenon of input congestion and output deficiency is serious in the inland ports of the Yangtze River System. Finally, some measures are put forward to improve the efficiency of inland ports in the Yangtze River System.