In this study, we collected soil samples from the freshwater Phragmites australis marsh at the Minjiang River estuary and constructed wetland soils with different salinities of 0‰, 2.5‰, 11‰, and 22‰ by adding artificial seawater and stabilizing for three months. These salinity values correspond to the ranges of fresh, oligohaline, mesohaline, and polyhaline water zones in estuarine tidal wetlands, respectively. We conducted indoor microcosm anaerobic incubation experiments and meanwhile added ammonium and nitrate to determine role of salinity in the impact of nitrogen additions on CH₄ and CO₂ production in estuarine tidal marsh soils. The results showed that the salinity and nitrogen form had significant effects on the activities of BG, CBH, NAG, PHO, PEO, and mcrA, the addition of ammonium and nitrate significantly increased activities of CBH, NAG, and mcrA in the soils with different salinities. Ammonium addition significantly increased CH₄ production rates in the fresh, oligohaline, and mesohaline water marsh soils by 21.9%, 23.6%, and 40.4%, respectively, but had no significant effect on polyhaline soil. Nitrate addition decreased CH₄production rates in the fresh, oligohaline, and mesohaline soils by 16.56%、15.56% and 19.28%, respectively, although the drop were not significant (P>0.05), nitrate addition significantly reduced CH₄production rates in polyhaline soil by 19.7%. Both ammonium and nitrate addition significantly increased CO₂ production rates in oligohaline and mesohaline soil, while did not significantly change the CO₂ production rates in the fresh and polyhaline soil. Under the nitrogen addition, the production rates of CH₄ and CO₂ were significantly positively correlated with soil pH, extracellular enzyme activities, and mcrA abundance, and significantly negatively correlated with salinity, SOC, Cl^-, and SO₄^2-. The results of random forest model prediction showed that under nitrogen addition scenarios, salinity, NAG, SO₄^2-, and pH had the greatest contribution rates to the production rates of CH₄ and CO₂. Our results indicate that the impact of nitrogen input on CH₄ and CO₂ production rates of estuarine marsh soils varies with salinity. In future, we should consider the influence of salinity gradients when making the strategies and measures to mitigate impact of eutrophication on greenhouse gas emission.