Located offshore from the mouth of the Changjiang River, which is the largest river in China and the third largest river in the world, the Changjiang Estuary is a multi-channel estuary with a triple bifurcation. The Deepwater Navigational Channel was created at the North Passage of the Changjiang Estuary during 1998–2010. Since the completion of project, the silting and back-silting problem is a serious threat in the Deepwater Navigational Channel. In order to reveal the sediment transport process in the Deepwater Navigation Channel of the Changjiang Estuary, hydrodynamic model coupled with sediment transport model was established by FVCOM in this paper. After the verification of flow field, salinity distribution and suspended sediment concentration, the model was utilized to simulate the distribution of sediment flux along the channel. It’s pointed out that sediment deposits more easily in the upper channel and the extent of silting at the right part (face to the sea area) was less than that at the left and middle parts in the transverse section. Through the decomposition of sediment flux into advection and tidal pumping flux, it’s found that the tidal pumping flux had more influence on sediment flux distribution along the channel. The direction of tidal pumping flux was seaward in the upper channel, and it changed into reversing direction at the lower channel. The magnitude of tidal pumping flux decreased along the channel. It’s shown that the impact of tidal pumping flux was more significant in the upper channel. The differences between tidal pumping sediment flux in spring tide and neap tide were significant along the channel. The maximum of seaward tidal pumping flux occurred in spring tide in the upper channel, while the maximum of upstream tidal pumping fluxes appeared in neap tide in the lower channel. The distributions of tidal-average tidal pumping flux also varied along the channel. The artificial structures in the Deepwater Navigational Channel which caused the change of topography and flow characteristics may be the reason of the intensive change of tidal pumping flux.