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• By introducing vegetation drag force inside the water body, a new method is proposed to estimate flow conveyance in compound channel with vegetated floodplains based on energy balance. • The energy loss caused by vegetation is derived and the relation between energy and discharge in a compound channel with vegetated floodplains is developed. • Compared to equivalent Manning's roughness coefficient, vegetation drag force can reflect the actual situation which is vegetation additional resistance is both on the river bed and the entire water body. Precise estimation of flow conveyance in a two-stage open channel with vegetated floodplains is a key prerequisite to the management of the river ecosystem and the creation of flood retention space. The presence of vegetation alters the structure of water flow and affects the discharge in a two-stage channel. Nevertheless, the effect of vegetation on flow conveyance is not studied separately in the previous flow discharge research. By conducting force analysis in a control volume with considering the vegetation drag force and quantifying the energy loss caused by vegetation blocking effect and the transverse velocity gradient, this paper proposes a new method to estimate flow conveyance in compound channel covered with vegetation based on the relationship which is the total energy loss is balanced by the total energy supplied by the local flow. Experimental data series are collected to verify the new method by comparing the measured and estimated discharges and it presents a good accuracy with 2.47% relative error. The new method is also compared with the other methods, which quantify the additional resistance of vegetation by using the equivalent Manning's roughness coefficient. The results indicate that both the vegetation drag force and the equivalent Manning's roughness coefficient can be used in flow conveyance estimation and dominantly influence the accuracy of the predictive method so that they need to be properly quantified and calibrated. And adopting the vegetation drag force is suggested here for the simplicity of calculation. [ABSTRACT FROM AUTHOR]