Nitrogen transfer processes and NO3− sources in the East China Sea (ECS) were analyzed using dual isotopes of NO3− and NO2−, the concentration and isotopes of dissolved O2 and N2 gases, nutrient concentrations, and the hydrological conditions. It was clear that the δ15N and δ18O values of NO3− in the Changjiang freshwater were 5.6–6.6‰ and 0.6–1.0‰, respectively, affected by human activities (fertilizer, sewage, and manure) and nitrification. Off the Changjiang Estuary to the ECS continental slope, the NO3− concentration was lower or exhausted in the upper water layers, where both available δ15N and δ18O values for NO3− were high related to phytoplankton assimilation. In the lower water layers, organic matter remineralization, nitrification, and coupled sedimentary nitrification and denitrification resulted in low NO3− isotope values. Moreover, in the upper water layers of the ECS continental slope, NO3− showed high δ15N and δ18O values and low Δ(15, 18) values affected by assimilation, nitrification, and N2 fixation. NO2− in the ECS was dominated by NH4+ oxidation, and NO2− oxidation plays an important role in depleting NO2− in δ15N values. An overall NO3− budget is built for the ECS shelf, indicating that open boundary exchanges of NO3− flux and isotopes through Kuroshio invasion and Taiwan Warm Current Water are comparable to outflow off the ECS shelf, and nitrogen transformation processes (such as NO3− assimilation and nitrification) play an important role in nitrogen cycle, and NO3− is modified on the ECS shelf.