The structural composition of an ecosystem or biological community will change as a result of changes in the external environment, or the change in the manner of conversion between internal matter and energy. According to the study of the structure composition of ecosystem or biological community, this association can be used to analyze the internal and external state. The diversity index is a simple and feasible method to describe the composition of the ecosystem or biological community, and has been widely used in ecology. In order to study and understand the structure changes of fishery community structure and marine ecosystem in time and space, this paper, based on the survey data of four-quarter fixed-point bottom trawl in 2000, using the Shannon-Wiener, Margalef and Pielou indices which were commonly used in marine ecology researches, adopted the clustering analysis method and the spatial projection method to describe and summarize the distribution and variation of seasonal fishery biodiversity in the middle and north of the East China Sea and the southern part of the Yellow Sea, and discussed the possible causes of seasonal variation in the number and weight of organisms, and analyzed the association between diversity and biomass weight and quantity. The results showed that the sites in each season could be divided into three groups with high, middle and low diversity. The distribution of each group was in the shape of point, line and block. The combination of groups is analogous to a “sandwich” structure with the center, interlayer and outer layer corresponding to high, medium and low diversity. The distribution of the “sandwich” structure in each season may be related to the physiological cycle migration of fishery resources. The center waters of the structure may correspond to the main range of most fishery biological migration. For example, the centers of four “sandwich” structures in spring correspond to the spawning grounds for Pseudosciaena polyactis, Larimichthys crocea, Pampus argenteus, Setipinna taty, Thamnaconus septemtrionalis, Scomber japonicus, Auxis rochei, etc.. The center of “sandwich” structures in summer, autumn and winter may correspond to the main feeding, fostering and overwintering grounds of fishery organisms. There were waters in all seasons with high and low diversity groups connected directly, and the diversities showed the spatially skipped-changing. The resource biomass of these waters was generally relatively low. In the waters with low total resources, species diversity will be high when the species is relatively balanced, and once a species of biomass is slightly increased it may lead to drastic fluctuations in diversity. It was also found that these waters are generally adjacent to the relatively high biomass waters, and the range of the waters was negatively related to the absolute biomass of the relative high biomass waters. It might be related to the aggregation degree of some dominant species. The dominant species with higher biomass had higher aggregation degree, and the aggregation range and influence were relatively small. The smaller the influence sphere of the dominant species, the smaller the range of fluctuation of the diversity of the surrounding low-biomass samples. On the contrary, the dominant species with low aggregation degree, but its influence sphere is relatively large, and the range of fluctuation of the diversity of the surrounding low-biomass samples is large. The average weight and number of species in spring and winter are consistent, but not in summer and autumn. This may be related to different life cycle processes such as spawning, growth and recruitment. The fish body of the main fishery resources in each season is a relative standard, and number of relatively large or small individuals is relatively few. Non-standard body size only occurs in the summer and autumn, which might be due to the gradual increasing of the recruitment of fishing populations. A relatively small number of recruitment comes from some earlier spawning groups in summer, while main of the recruitment of the year comes in the fall. As a result of recruiting, the lean body appears in the highly diverse groups of summer and autumn. The overweight body in the middle and high diversity groups of summer might be because of the non-spawning broodstocks, whose body was always fat to ensure the next generation with enough nutrition. They also might include a small number of delayed spawning, or skipped-spawning fish in the stage of self-absorption, which were always with fat body. Regardless of weight or mantissa, the cases that diversity index decreased with the increase of biomass were more than the cases that diversity index increased with the increase of biomass. Most of the increase in biomass was not because of the increase in the number of species, but was likely to be due to the increase of biomass of very few dominant species, resulting in a decrease in the homogeneity of species and a decline in biodiversity. The positive association of diversity indices with mantissa was significantly higher than the positive relationship with weight, probably due to the increase in the number of organisms in most cases were due to the increase in the number of species resulting in higher diversity, while the increase of weight was mostly because the dominant species continued to expand, leading to the decrease of diversity.