This paper studies the flow structure and the bedload transport regime in backwater flows, to provide a theoretical support for solving the sediment transport and bed scour problems in rivers or reservoirs with backwater. The bedload transport rates under different conditions are analyzed first on the basis of theoretical analysis, measurement comparison and flume experiment, and it is pointed out that the existing formulas for the bedload transport rate are not applicable for the bedload transport rate in backwater flows. Next, the flow structure in a non-uniform flow is observed by flume experiments, and by introducing the backwater degree index, the quantitative relation between the relative bed shear stress and the backwater degree is obtained. Finally, the formula for the bedload transport rate applicable for the reservoir channel segment with backwater flows is obtained through measurements and flume experiments.