The Yangtze finless porpoise, a subspecies of narrow-ridged finless porpoise, is only distributed in the middle and lower reaches of Yangtze River and two large river-connected lakes-Poyang and Dongting Lakes. With the depletion of fish stocks in Yangtze River, prey availability has become the most important factor determining the survival of the finless porpoise. However, the community structure of the fish in primary habitat of the finless porpoise is far from being fully understood. In the mainstem of Yangtze River, the highest density of porpoises was observed in the Anqing section. Several field surveys in the Anqing section have indicated that the confluence of Yangtze and Wanhe Rivers is one of the primary habitats of the porpoise. Therefore, the confluence and its adjacent regions were selected as our study area, and field surveys were conducted monthly from September 2013 to August 2014. A total of five transects were set. The length of each transect and interval between transects were 400 and 200 m, respectively. To avoid sampling bias due to the use of a single fishing method, multi-mesh drift gillnets and electronic trawl nets were used. The former (length × height:100m × 2 m) was mainly used for upper fish and had three mesh sizes:10, 20, 40 mm. The latter, with a voltage of 12 V, was mainly used to collect lower and demersal fish. The length, height, and mesh size of the trawl net were 3 m, 1 m, and 10 mm, respectively. In each transect, the electronic trawl net was towed by a boat for 400 m, and the speed of the boat was maintained at 1 m/s by using a GPS. The multi-mesh drift gillnets were tied to a boat, which drifted with the water current for 10 min. All fish collected using the two methods were brought back to the lab and identified to the species level. For each individual, body length and weight were measured. A total of 35 fish species were collected. When compared with historical data, it became apparent that the species diversity in this area has decreased dramatically, and the fish show an obvious tendency towards miniaturization. Among the five transects, species number was the highest in the confluence, and the main dominant species were upper fish (Hemiculter leucisculus and H. bleekeri); however, most of the other transects were dominated by demersal fish (Pelteobagrus fulvidraco and P. eupogon). ANOVA indicated that the total individual number and weight of the catch in the confluence were not significantly different with other transects, but the total species number was significantly higher than those at transects 1 and 5. Further analyses of upper, lower, and demersal fish showed that a significant difference was detected only in the upper fish species, and the individual number and weight of upper fish were significantly higher than at other transects. Therefore, we concluded that the greater abundance of upper fish in the confluence was the primary reason for its being inhabited by the finless porpoise. The results of this study can not only help us keep track of changes in fish stocks, but also have important implications for the ex-situ and in-situ conservation of the Yangtze finless porpoise.