To understand the long and consecutive variation characteristics of fishery species structure in the East China Sea and the Yellow Sea, using the method of clustering and average trophic level analysis, stages and features of main fishery species structure variation have been summed up and analyzed, and the main fishery species have been classified into groups, and the relation between average trophic level and fishery resources density has been analyzed, based on 14-consecutive-year fishery resources survey data in autumn from 1999 to 2012 by paired bottom trawl. The results show that the development of fishery species structure could be divided into 3 stages, including the early stage of jellyfish bloom(1999—2003), the outbreak stage of jellyfish bloom(2004—2007)and the later stage of jellyfish bloom(2008—2012). In the early stage, variation period of fishery resources is 2 years; but in the later stage the period changed to 1 year. With 5 years of development after jellyfish bloom, it seemed that fishery species structure recovered to a stage close to the early stage of jellyfish bloom. By clustering method the main fishery species could be classified into 6 species groups, including blooming(e. g. Stomolophus meleagris), advantage(e. g. Trichiurus japonicus and Pseudosciaena polyactis), unusual(e. g. Trachurus japonicus), common(e. g. Psenopsis anomala, Pampus argenteus and Setipinna taty), jellyfish accompanying(e. g. Cyanea nozakii and Aurelia aurita)and rare(e. g. Scomber japonicus, Harpadon nehereus etc. )species groups. By comparing quantities of species before and after jellyfish bloom, the species of rare species group could be classified into 3 groups: one with species whose quantity changed from high to low(e. g. Harpadon nehereus, Coelorhynchus multispinulosus etc. ), one changed from low to high(e. g. Scomberomorus niphonius, Solenocera melantho etc. )and the other with no change(e. g. Scomber japonicus), who in these groups had some characters of indicator species for ecosystem health state. Based on the data of 14 years, the relation between average trophic level and fishery resources density was significantly negative(P< 0. 001), whose equation was TL=-0. 896 5· ln(CPUE)+ 14. 142 1(TL means average trophic level, CPUE means catch per unit effort). The relation shows that the average trophic level of the marine ecosystem decreases with the increase of its total resources quantity, and vice versa.