The seasonal hypoxic zone off the Changjiang estuary on the East China Sea (ECS) shelf is one of the largest coastal hypoxic zones in the world, which undergoes remarkable interannual variation. It is significant to understand the role of sediment oxygen consumption (SOC) played in the development of hypoxia. A pelagic‒benthic coupled model is applied to quantify the SOC via the degradation of oceanic particulate organic carbon. The model takes into account the porewater advection, molecular diffusion and bioturbation by macrobenthos. It is found that the SOC in summer shows great heterogeneity. By comparing SOC to the water oxygen consumption (WOC) below the pycnocline, the contribution of SOC is generally below ∼40% in the hypoxic zone. The spatial distribution of SOC in summer is relatively steady from year to year, while the high WOC patches explain more about the interannual variation in the hypoxic zone. WOC rather than SOC drives the variation of hypoxia. In non-depositional areas, milder hydrodynamics are favorable for both the higher WOC and bioturbation-induced benthic oxygen flux but substantially suppress the porewater advective flux, which results in the net lower contribution of SOC to hypoxia. On the contrary, the stronger water column mixing and weaker solar radiation result in the higher contribution of SOC compared to WOC but less probability for hypoxia. This finding may shed light on other pelagic-benthic coupling processes in coastal shelf seas where hypoxia occurs on permeable sediments.