The waters of the Changdao Archipelago are located at the confluence of the Yellow and Bohai seas, which have high species diversity and spatial and temporal heterogeneity. This area is an important route for migratory fish and macroinvertebrates to enter the Bohai Sea for spawning or to leave the Bohai Sea southward for overwintering. In recent decades, with increasing human activities, fishing pressure, and ocean pollution, the ecosystems of the Yellow and Bohai seas have become fragile with many fishery species evolving towards miniaturization and precociousness. Important fishery resources are unable to fulfill the minimum requirements during the fishing season, and the support function of the Yellow and Bohai seas is diminishing. Research on fishery species in the waters of the Changdao Archipelago is less focused on their composition, community structure, and fishery biological health evaluation. To understand the species composition and diversity of demersal fishery species in the waters of the Changdao Archipelago and to identify keystone species that play important regulatory roles in the biological community, we analyzed the biological diversity and identified the dominant species based on the Changdao Archipelago fishery resource survey data from March to December 2021. Keystone species were determined by food web topology and social network analysis, and the fishery biological health status was determined based on the 2021 survey data. A total of 38 species of fish (mainly warm-water, demersal, and low-value fish) and 50 species of invertebrates (mainly small crustaceans) were caught in the area. There were obvious seasonal variations in the composition of the dominant species, with invertebrates, such as Alpheus japonicus and Oratosquilla oratoria, dominating in the spring, Chaeturichthys stigmatias and O. oratoria in the summer and autumn, and only A. japonicus and C. stigmatias in the winter. The species Margalef richness index (R) was highest in the summer, and the Shannon-Wiener diversity index (H´) and Pielou evenness index (J´) were highest in the autumn, in the waters of the Changdao Archipelago. To further investigate the food web topology of the bottom fishery community in the waters of the Changdao Archipelago, and to identify keystone species, seasonal changes in the topology of the study area were analyzed. Based on field survey data, the main species (IRI > 100) were constructed. The area contained 13–23 main species (S) and 32–113 feeding relationships (L) in four seasons. The node density (Dd) ranged from 0.18–0.41, link density from 2.46–5.65, connectance (C) from 0.18–0.28, clustering coefficient (Cl) from 0.334–0.401, and weighted clustering coefficient (W-Cl) from 0.276–0.373, consistent with the interspecific feeding relationships in communities under natural conditions. There were significant seasonal variations in each topological index. Based on the topological structure index, we analyzed the robustness of keystone species at the bottom of the food web in the waters of the Changdao Archipelago. Using different removal methods, we found that these three species have differences in maintaining the robustness of the food web. To study the importance of keystone species, species were removed in ascending and descending order according to the node degree (D). Under the descending order of removal, the stability of the food web showed a downward trend, showing a "staged" change of first increasing and then decreasing. This change may be due to the reconstruction of the food web caused by the loss of some species. Even if new feeding relationships are created among other species, the number of corresponding feeding relationships decreased exponentially, while feeding relationships with ascending removal patterns showed an inverted U-shaped trend with a significantly slower rate of decline. The most important species in the food web were removed first in descending order, which had the greatest effect on the stability of the food web and the number of feeding relationships. Among them are species that play important roles in the robustness of the food web—C. stigmatias, Pennahia argentata, A. japonicus, and O. oratoria are both dominant and keystone species. The keystone species in the waters of the Changdao Archipelago are diverse and small, as most of the bottom organisms in the area are omnivores with diverse feeding relationships and include many migratory species in addition to native species, which leads to the diversity of keystone species—C. stigmatias, P. argentata, A. japonicus and O. oratoria are both dominant and keystone species. The keystone species are characterized by diversification and miniaturism. When keystone species were removed from the food web, the linkage robustness and number of feeding relationships decreased significantly, indicating that keystone species play important roles in maintaining the stability of the food web. In winter, keystone predator species change from O. oratoria and P. argentat to C. stigmatias, and A. japonicus changes from the keystone prey species to the keystone intermediate species. Niche replacement of keystone species leads to the simplification of the bottom of the food web and, to some extent, increases the vulnerability of the bottom community structure in the waters of the Changdao Archipelago. Therefore, in future studies, dynamic monitoring and protection of keystone species should be strengthened to maintain their robustness function in the food web, to maximize the protection of natural resources in the waters of the Changdao Archipelago.