The channel connecting the Poyang Lake and the Yangtze River is an important channel for most migratory fish to complete their life cycle process, and so has an important ecological function for the conservation and diversity of fish resources in the middle and lower reaches of the Yangtze River. In this study, acoustic detection, remote sensing, and three-dimensional hydrodynamic simulation were combined to understand the spatial distribution and habitat status of fish with different body length in the channel connecting the Poyang Lake and the Yangtze River through the winter period. Firstly, the single factor habitat suitability index (HSI) curves of water depth, flow velocity, and slope of three fish groups with different body length were drawn, and then the product method was used to establish the habitat suitability model. Finally, the habitat suitability of fish in different sections of the channel connecting the Poyang Lake and the Yangtze River was compared and evaluated. The results showed that the average length of fish in the channel was 10.1 cm, and the fish were mainly distributed in Hukou, Mountain Xie, and Pingfeng area. The most suitable water depth range for fish groups with body length of 1–20 cm was 3.06–4.59 m and 9.18–12.24 m, with a flow velocity range of 0.05–0.13 m/s and slope range of 0–2.23°. The habitat suitability curves of water depth, flow velocity, and slope of fish that were sized 20–40 cm and over 40 cm were unimodal, and the most suitable range of water depth, flow velocity, and slope of the 20–40 cm fish group were 9.18–13.77 m, 0.05–0.13 m/s, and 0–2.23°, respectively. For fish with body length over 40 cm the most suitable ranges of water depth, velocity, and slope were 13.77–15.3 m, 0.10–0.13 m/s, and 0–2.23°, respectively.