There are many bending branched shoals, which are the main obstacles of navigation, in the upper reaches of the Yangtze River, and the reaches are also the main breeding areas of endangering fishAcipenser sinensis. Currently, waterway regulation projects in this region seldom consider the impact on aquatic habitats. In addition, existing habitat assessment methods are mainly based on the weighted usable area (WUA) of habitats in the instream flow incremental methodology (IFIM). In this study, we took the bending branched shoal in the upper reaches of the Yangtze River as a case study, considering the zoning characteristics of the spawning grounds ofAcipenser sinensiswith different functions. On the basis of patch area ratios of habitat, fragmentation index and habitat connectivity index, a comprehensive evaluation model of fish habitat were constructed, and the effects of submerged spur dikes on the habitat ofAcipenser sinensiswere studied. Results indicated that appropriate layout of submerged dike could improve the environmental quality of the habitat ofAcipenser sinensisobviously. In addition, the number of patches was proportional to the length of submerged dikes, and the area ratio of patches and the fragmentation index of habitat were inversely related with the number of dams, while the connectivity index of habitat was mainly affected by the number of dams. From the point of protecting endangered species, the number and length of regulation projects for the bending braided shoals hindering the navigation should be controlled properly. In addition, the comprehensive evaluation model of fish habitat based on the reproduction and life habits of endangering species proposed in this study can overcome the problems currently existing in the habitat evaluation only according to the WUA, and it is more suitable for the environmental quality evaluation of fish habitat.
