The momentum transfer coefficient is an important parameter for determining the apparent shear stress at the vertical interface between the main channel and its associated flood plains, the cross-sectional mean velocity and the discharge capacity in compound channels. In this article, under the Boussinesq assumption and through analyzing the characteristics of velocity distribution in the interacting region between the main channel and its associated flood plain, the expression of momentum transfer coefficient was theoretically derived. On the basis of force balance, the expression of vertical apparent shear stress was obtained. By applying the experimental data from the British Engineering Research Council Flood Channel Facility (SERC-FCF), the relationship between the momentum transfer coefficient with the relative depth and the ratio of the flood plain width to the main channel width, was established, And hence the conveyance capacity in compound channels was calculated with Liu and Dong’s method. The computed results show that the momentum transfer coefficient relationship obtained is viable.