Community structure of fishery biology in the Yangtze River estuary and its adjacent waters were examined based on data collected from bottom trawl surveys in June, August and October, 2006. It was inscribed that there are 207 fisheries species, which were mainly composed of warm water and warm temperature species, cold temperature species, such as Lophius litulon and Liparis tanakae, also were found in the surveys and became dominant species in fisheries community. Fishery biology diversity increased, the period of shifts of species was reduced, and some migration species were not collected in the surveys. Some ecological groups with lower economic value, smaller size, simpler age structure and lower tropic level were absolutely predominant positions in the Yangtze River estuary and its adjacent waters. The number of fishery biology species in 2006 was higher than that in the 1980′s, but the total biomass and the number of individual was about 8% of 1980′s surveys. The higher fishery biomass was found in the north part, central part and coastal waters of the survey area, adversely, the higher diversity of fishery biology was found in the southern survey area and outer waters, so it was hard to maintain higher fishery production when higher diversity was evenly distributed in fishery biology community.