Abstract: The Yangtze River estuary is the major production regions of larval eels in China, and it is also the most important place for feeding and nursing place for fishes. In order to clarify the species diversity and damage rate of fishes by-catch in elver nets in the Yangtze Estuary, this article analyzed 11870 fish samples collected by elver nets during the eel fry flood season from 2017 to 2019. The results showed that 43 samples contained 114388 fishes by-catch in elver nets, 54 species were identified, belonging to 13 orders, 27 families and 46 genera. Among them, Perciformes accounted for 40.74% of the total species, and marine, carnivorous, demersal and small fishes accounted for 44.44%, 74.07%, 70.37% and 48.15%, respectively. Odontamblyopus lacepedii was the first dominant species, accounting for 77.07%; Cynoglossus joyneri, Coilia nasus and Konosirus punctatus were also the dominant species in individual years. According to the difference of fish assemblage, March and April, January and February can each be combined into one group. The major characteristic species of two groups were 5 and 6, and the major divergent species were 10. The average body length was (73.77±38) mm of 54 species. Fish resources of the early life history stages account for 96.65% of the total samples, many of which are larvae of local economic fishes. There were 16470 eel elvers in the sample, and the average damage rate of fishes by-catch in 3 years was 7.58, which was higher than 6 years ago. Attention should be paid to the damage caused by fishing eel elvers to other fishes’ larvae.