A mathematical model based on advection-diffusion theory is established to study the non-equilibrium sediment transport process in vegetated channels. The effects of vegetation on velocity distribution and sediment diffusion coefficients were considered, respectively. Validation against experimental data from flume studies confirms the model's ability to accurately predict the longitudinal sediment deposition rate and the vertical distribution of suspended sediment concentration (SSC). A comparative analysis of three sediment diffusion coefficient formulations indicates that the linear-exponential formula provides a more precise estimate of εsz, and the linear-exponential formula performs well in predicting the turbulent diffusion coefficients of both rigid and flexible vegetation when gently swaying. Moreover, the distance required for SSC to regain equilibrium is influenced by the submergence level of the vegetation canopy. At lower submergence levels, the canopy shear vortices significantly affect the vertical exchange of sediment, and the sediment diffusion coefficients exhibit pronounced stratification near the vegetation canopy. An increase in vegetation density at these lower submergence levels intensifies the shear vortices, thereby extending the distance needed for SSC to reach equilibrium. At higher submergence levels, the impact of canopy shear vortices is lessened, which reduces sediment diffusion coefficient stratification characteristics, and the flow is similar to rough boundary layer flow. An increase in vegetation density increases flow resistance, which shortens the distance required for SSC to attain equilibrium. However, further efforts are required to explore turbulent characteristics with highly flexible vegetation motion and the grain size distribution of non-uniform sediments in vegetated flows.