The main urban area of Chongqing reach is located at the fluctuating backwater area of the Three Gorges reservoi. The operation of the reservoir has a significant impact on the erosion and deposition of this reach, not only the total amount and scope, but also the period in one year. In this paper, a two-dimensional hydraulic mathematical model was built in order to simulate the sediment deposition in this reach. The calibration was carried out by using some series of field data to provide the accurate parameters, such as roughness, sediment capacity. And values of roughness, coefficient and index of sediment carrying capacity, saturation coefficient of deposition and erosion are suggested after the calibration.