Nutrient exchanging with the East China Sea (ECS) plays an important role in nutrient structure and primary production in the Yellow Sea (YS). Due to the lack of simultaneous observations of current velocities and nutrient concentrations, the temporal and spatial of nutrient exchanges across the interface between the YS and the ECS (Section YE) are still unclear. In this study, a 3-D physical-biochemical coupled model was used to the flux of the dissolved inorganic nitrogen (DIN) across Section YE after reproducing the seasonal variations and distributions of physical and biochemical variables. The results showed that DIN was transported from the ECS to the YS all throughout the year. The DIN imported into the YS across YE in summer was the largest in the four seasons, accounting for 38% of the total annual amount. The seasonal variations of DIN flux were attributed to the seasonal variations of the velocity across Section YE instead of those of DIN concentration. However, the spatial differences of seasonal variances of DIN flux were controlled by both seasonal variations of velocity and DIN concentration. For the YS, exchanging with the ECS contributed 64% of the amount from all the external sources. The annual amount of DIN from open boundaries was larger than the river input and comparably similar to the atmospheric deposition for the YS.