The long-term changes in fish ecological structure and fishery resources were studied in the Eastern Seas of China (Bohai Sea, Yellow Sea, and East China Sea) and the South China Sea based on 1983-2013 catch statistical data, using fish trophic level (TL), the FiB index, and the main fish cluster caught by Chinese fishing vessels. A correlation analysis of the change in fish ecological structure based on fishing method was also conducted. The results show that mean TL has declined among the 25 main fish species caught in the Eastern Seas of China. The contribution of carnivorous fish in the lowest class to total catch has increased 60%, the contribution of carnivorous fish in the middle class to total catch has increased 129%, and the contribution of carnivorous fish in the advanced class to total catch has decreased 51%. No changes in mean TL have occurred in the South China Sea; however, the contribution of carnivorous fish in the lowest class to total catch has decreased 6%, the contribution of carnivorous fish in the middle class to total catch has decreased 43%, and the contribution of carnivorous fish in the advanced and middle classes to total catch has increased 198%. These results suggest that fisheries resources in the Eastern Seas of China, but not those in the South China Sea, are declining.