Previous studies have highlighted the salinization caused by the use of seawater to flush toilets and industrial wastewater entering the urban wastewater systems in coastal areas. Thus, in this study, the effect of salinity on N2O emissions during the partial nitrification process, as well as the emission mechanism, was investigated using a partial nitrification system of wastewater as the research object. The results showed that (1) the increase in salinity decreased the oxidation rate of NH4+ and the formation rate of NO2− during partial nitrification; (2) the increase in salinity increased the N2O emissions during NH4+ oxidation and NH2OH oxidation and decreased the formation rate of NO2−-N during hydroxylamine oxidation; (3) the total N2O emissions during hydroxylamine oxidation were less than those during ammonia nitrogen oxidation, and a greater amount of NO2− was reduced to N2 instead of N2O during hydroxylamine oxidation; and (4) a novel finding was that, during partial nitrification with the available organic matter, the N2O emissions via heterotrophic denitrification by heterotrophic bacteria should not be ignored, and the increase in salinity can increase the N2O emissions generated via heterotrophic denitrification. These results would provide a theoretical basis for reducing the N2O emissions in the wastewater treatment process.