Fish is considered to be the important component of biodiversity of aquatic ecosystems. To explore the characteristics of fish communities in Jiangsu Province, a survey of fish communities in 148 surface water environmental monitoring sections was conducted during April to May 2020 using environmental DNA metabarcoding technology. A total of 418 fish OTU were detected in the environmental DNA samples, and 46 species were annotated into 10 orders, 14 families and 32 genera, and 27 species of which are Cypriniformes, accounting for 81.2% of the sequences. The results showed that the fish diversity of the Huai River basin is relatively better, followed by the Yangtze River basin and the Taihu Lake basin. The result has provided basic information on the structural characteristics of fish communities in surface water monitoring sections in Jiangsu Province, and gave a reference to the application and promotion of environmental DNA technology in the field of environmental monitoring.