Abstract: Hydrological connection plays an important role in maintaining biodiversity and ecosystem function. In order to explain the effect of internal hydrological disconnection and response of fish communities, we selected a typical hydrological disconnection lake in middle reaches of Yangtze River-Bao’an Lake as the study object. Field sampling was conducted in Xiaosihai Lake (part of Bao’an Lake, complete disconnection), Biandantang Lake (part of Bao’an Lake, semi-disconnection), Qiaodun Lake (part of Bao’an Lake, semi-disconnection) and the main lake in both summer and autumn from 2019 to 2020. We compared and analyzed the differences of fish communities and functional diversity among those lakes using the multiple statistical methods. Result showed that the fish community structure in the complete disconnection lake had been changed significantly, which species number (15±3) was significantly lower than that in the semi- disconnection lake (22±3) and the main lake (23±3; P<0.05); abundance increased while the biomass decreased; the species richness index, the Shannon index and the Simpson index were significantly lower; and functional richness index, functional dispersion index and functional evenness index were also significantly lower the other lakes (P<0.05). However, the fish community structure in the semi-disconnection lake had no significant difference with that in the main lake. The Permutational multivariate analysis of variance and non-metric multidimensional scaling analysis also showed that the fish community in the complete disconnection lake significantly distinguished from the semi-disconnection lakes and the main lake (P<0.05), while there was no significant difference between the fish communities of semi-disconnection lakes and main lake was closer. Our study found that the internal hydrological disconnection in lake also has an important impact on the composition of fish communities, and restoring the free hydrological connectivity within lake was crucial to ecological management and biodiversity conservation.