(1) Background: Increased attention has been paid to atmospheric nitrogen (N) deposition caused by human activities. N deposition quantity has seriously affected plant productivity and greenhouse gas emissions in wetlands, but the effects of N deposition frequency remain unclear. (2) Methods: We assembled microcosms, which contained vegetative individuals (ramets) of Hydrocotyle vulgaris and soil and subjected them to three frequencies (N addition 1, 2, and 14 times during the experimental period) crossed with three quantities (5, 15, and 30 g N m−2 yr−1) for 90 days. (3) Results: The quantity of N addition significantly increased the root, stem biomass, and ramets number of H. vulgaris, but decreased the spike biomass. N addition quantity significantly promoted N2O emission and inhibited CH4 emission but had no significant effect on CO2 emission. The increasing frequency of N addition significantly promoted the root-to-shoot ratio and decreased N2O emission under high N addition quantity. (4) Conclusions: In conclusion, N addition alters the reproductive strategy of H. vulgaris and enhances its invasiveness, promoting N2O emission but not the CO2 equivalent of the H. vulgaris-soil system.