Abstract: Fishery is an important component of the food supply chain. It is important to study the economic efficiency of fishery and to understand the current situation and problems in the exploitation of fishery resources in order to improve the economic efficiency of fishery and promote sustainable development. Based on the panel data of 11 provinces (cities) in the Yangtze River Economic Zone from 2012 to 2021, this paper analyzed the economic efficiency of fishery and its differences when combining the super-efficient SBM model, super-efficient Malmquist index and Theil index analysis. The results showed that, the economic efficiency of the fishery industry in the Yangtze River Economic Zone had been increasing in general, gradually showing a trend of the highest efficiency in the downstream; the economic efficiency value of the fishery industry tended to be 1, and the utilization rate of fishery input resources was high in each region; the overall development of the fishery industry was relatively balanced, and the differences in the economic efficiency of the fishery industry were mainly formed by the intra-regional differences. Based on this, the future development of fishery in the Yangtze River Economic Zone should focus on technological innovation in aquaculture fishery, expansion of aquaculture scale and coordinated and balanced development between regions.