Hengsha Shoal is located in the Yangtze River estuary, which is rich in biological resources. However, in recent years, owing to construction in the estuary, the community structure of aquatic species in this area has changed. To understand the community structure of swimming species in the Hengsha Shoal and adjacent waters of the Yangtze River Estuary to determine the construction effect, this study carried out a bottom trawl data survey in the summer of 2019. The community structure was analyzed by studying the dominant species, species diversity, and community structure characteristics. The results showed that there were 68 swimming species in summer, including 29 fish species, including 8 orders and 16 families; 30 arthropod species, including 2 orders and 15 families; and 9 mollusks species including 4 orders and 7 families. The species composition mainly comprised arthropods and fishes. The dominant species were Exopalaemon annandalei, Palaemon gravieri, and Chaeturichthys stigmatias, which are mainly small, low nutrition, and short life cycle species. The population characteristics showed a trend of miniaturization and low nutrition. The survey showed that the biodiversity index in this area is low, the community structure of swimming species is generally unstable, greatly disturbed by the environment, and there are obvious spatial differences. The results of cluster and ordination analyses showed that the investigated area can be roughly divided into two groups, and the differences of species community structure between the two groups were very significant (R=0.825, P<0.01). The main contributing species of the differences between the groups were E. annandalei, P. gravieri, C. stigmatias, and Larimichthys polyactis, and salinity and water temperature were the main factors that contributed to differences of community structure. Generally, recent beach reclamation and construction of a deep-water channel may have impacted the community structure of swimming species in Hengsha waters.