Global change can easily cause the wetland ecosystem structure and function to be damaged by alien species. Former studies on Spartina alterniiora invasion only focused on the effect of aboveground communities, ignoring the potential regeneration of soil seed banks. Therefore, the study aimed to find the key resources that limit the S. alterniiora invasion and the regulation mechanism for S. alterniiora regeneration. Through investigating the S. alterniiora communities with different invasion stages, we studied the structure and composition of the aboveground communities and the soil seed banks, in response to the soil properties and water and nitrogen addition. The dominant competitive advantage of S. alterniiora was mainly affected by the aboveground biomass, which was regulated by soil NH4+-N and moisture content. Although the richness was same in the soil seed banks under the S. alterniiora communities with different coverage, S. alterniiora seeds maintained its specific competitive dominance. The niche breadth of S. alterniiora and the niche overlap between S. alterniiora and Tripolium pannonicum was the highest under low aboveground coverage. The soil seed bank germination experiments showed that the S. alterniiora density decreased when the soil nitrogen concentration exceeded 1 g/ kg, while the density of native species E. crusgalli and T. pannonicum decreased when the water depth above the soil surface exceeded 2 cm. The successful naturalization of S. alterniiora invasion regulated by nitrogen-water coupling is a bet-hedging of the niche and fitness differences between invasive and native species in the coastal salt marsh of eastern China.