Nitrous oxide (N2O) is a potent greenhouse gas and a strong ozone‐depleting substance. Ocean is an important natural source of atmospheric N2O, which has attracted increasing attention recently as to understand the biogeochemical cycles of nitrogen in marine systems. Nitrification is one of the major N2O production pathways during which N2O is produced as a side product and hydroxylamine (NH2OH) is produced as an obligate intermediate. However, few studies have reported the NH2OH variability in natural seawater and its relationship between N2O remains ambiguous. In summer 2022, spatial distribution and influencing factors of N2O and NH2OH in the northern South China Sea (SCS) were investigated. Dissolved N2O varied from 5.79 to 34.80 nmol L−1 in water column and generally increased with water depth above 800 m. N2O was correlated with dissolved oxygen and nitrate, inferring that N2O was mainly produced via nitrification. NH2OH varied from below detection limit to 3.91 nmol L−1. The adoption of multiple standard additions can largely reduce the bias in NH2OH measurement. Structural equation modeling showed that NH2OH has a potential effect favoring excessive N2O. Surface N2O saturation ranged between 102% and 278%, indicating that the northern SCS was a net source of atmospheric N2O in summer.