The flow resistance and sediment transport in backwater condition is very important in hydraulic engineering. Through generalized flume experiment, we measured the flow velocity using Acoustic Doppler Velocimeter (ADV) and analysed the flow resistance and bed shear stress in the presence of backwater in river channel. Result shows that in backwater condition, the velocity distribution along vertical direction is much more homogeneous than that in uniform flow condition. The coefficient for describing the non-uniform flow increases when backwater intensifies, but still follows the logarithmic distribution. Friction velocity decreases with the depth of water increases, and the flow resistance increases with hydraulic radius and the coefficient for describing the non-uniform flow. Finally a formula is fitted between the bed shear stress index and the backwater degree index.