On the basis of the hydrology observed data and hydro-acoustically surveyed data in the reach of Yangtze River from Jiangkou Town to Yuanshi Town, the preference of the fish in the natural channel to the water velocity and depth is analyzed by the method of interpolation in air space of water depth and velocity corresponding to the fish density and fish size. The results show as follows: Different sized fishes have different preferences to the water velocity and depth. Smaller fishes prefer lower velocities and wider range of velocity, while larger fishes prefer higher relocities and narrower range of velocity. The depths smaller fishes enjoy are higher than those larger ones do; the range of the depths smaller fishes enjoy is more than that larger ones do. The fish density is not directly related to the water velocity, but to the depth, fish density is higher in the deeper water. The distribution features of the water velocity and fish density are different around the island in the reach of Jiangkou Town, which shows due to the diversity existence of velocity near the island may supply more suitable environments for fish. This preliminary study could provide some references to the assessment of the habitat suitability and ecology function of a river