This paper collects the data about measured terrain, hydrology and track line of ships of Heshang rapids in perennial backwater area of the Three Gorges reservoir, establishes the mathematical model, analyzes the channel condition variation in the flood season, and gains the critical discharge for ships ascending Heshang rapids. The results show that the channel condition of Heshang rapids in the flood season is improved, vertically-averaged flow and slop decreases, and water depth and width of navigation increases. The critical discharge for the 10 000DTW fleet and 3 000DTW ship increases, and the shipping efficiency in Three Gorges reservoir area is improved.