Recently, many river channels tend to be densely vegetated due to regime shifts in hydrological, fluvial and ecological processes. It is a critical engineering issue for flood control and management to evaluate the conveyance capacity of vegetated channels. In this study, an equivalent Manning's coefficient n(v) of vegetation canopy drag in an open channel of compound cross section with alternatively arranged floodplain is analyzed by using a two-dimensional two-layer (2D2L) model. It is found that n(v) monotonically increases with increasing discharge when vegetation is emerged. On the other hand, n(v) gradually decreases with discharge in the case of submergent vegetation. The numerical solutions of flow structure and n(v) is compared with experimental data to verify the model and satisfactory agreement between the analysis and the experiment is recognized.