The Chongming Island is located at the estuary of the Yangtze River. There are dense rivers and abundant fish resources on the Chongming Island, however, illegal fishing continues despite prohibitions, seriously affecting the level of the fish resources. Besides, fish diversity is an important indicator for aquatic ecology conservation. For evaluating and revealing fish resources and diversity in Chongming Island in Shanghai and reveal fish diversity, a quarterly survey was conducted in 24 sampling sites in the rivers of the Chongming Island from June 2020 to May 2021 which integrated environmental DNA technology and traditional fishing method. In this survey, a total of 78 fish species were detected, covering 13 orders and the Cypriniformes was the dominant species, accounting for 44% of total species found. The annual Shannon-Wiener diversity index calculated based on fish samples was 2.08, and the annual Shannon-Wiener diversity index calculated based on environmental DNA data was 2.96 respectively, indicating that the Chongming Island is rich in fish diversity. The common dominant species identified by the two methods were Parabramis pekinensis, Pseudobrama simoni, Pseudorasbora parva, Rhinogobius giurinus and Acheilognathus macropterus, indicating that the fish community structure in the rivers of Chongming Island is dominated by freshwater fish. The Principal Coordinate Analysis and the PERMANOVA test indicated that there are differences in fish composition between the community of East and West community (R²=0.101 2,P=0.027 6). We suggest that environmental DNA technology should be used as an important supplementary means for the investigation of fish resources and diversity. This study reported the existing status of fish resources and diversity of Chongming Island and provided basic data for rational utilization and conservation of the fish resources on the Chongming Island.