By transporting deep, nutrient-rich waters to the euphotic zone, coastal upwelling plays an important role in global ocean primary production and biogeochemical cycles. The Qiongdong Upwelling (QDU) is a typical upwelling system in the northern South China Sea. However, the spatial and temporal variations, and its budget of nitrogen in the QDU have not been well characterized. Applying a validated physical-biogeochemical coupled model, this study examines the dynamics of nitrogen in the QDU during 2010. The QDU initiated in mid-June, reached maximum intensity around mid-July, and relaxed in late July, creating a cold, nutrient-rich band extending off the eastern coast of Hainan Island. At its peak, surface nitrate concentrations reached 3.0–4.0 mmol m⁻³ nearshore, with a subsurface concentration of 6.0–8.0 mmol m⁻³ at 30 m depth—significantly higher than offshore waters. Ammonium levels remained depleted (<0.05 mmol m⁻³) during active upwelling but accumulated (>0.4 mmol m⁻³) during the relaxation phase. The elevated nutrients stimulated phytoplankton growth, resulting in surface chlorophyll-a peaks above 5.0–6.0 mg m⁻³. Time-series analysis revealed that nutrients responded almost instantaneously to upwelling pulses, whereas phytoplankton exhibited a 3-day assimilation lag, and zooplankton followed with a 7-day grazing lag. A nitrogen budget constructed for the upper 30 m upwelling core revealed that vertical transport was the dominant source, contributing 56% (12.1 × 10⁹ mmol d⁻¹) of total nitrogen input, followed by lateral advection from the southern boundary (43%) and negligible riverine input (1%). Nitrogen outputs were primarily driven by net biological consumption (65%), followed by offshore export through the eastern (30%) and northern (5%) boundaries. This study improves our understanding of nitrogen cycling in coastal upwelling systems and underscores the importance of physical-biological interactions in controlling ecosystem productivity.