Salinity and interspecific interactions are the main factors affecting community assembly of wetland ecosystems. However, most previous studies focused on the interaction between adult plants, and our understanding of their interspecific interactions at regeneration stage is still limited. Chongming Dongtan National Nature Reserve is a wetland of importance in the Yangtze River Estuary. The invasion of Spartina alterniflora has caused significantly negative impacts on native Scirpus mariqueter and the local ecosystem. This study examined the effects of salinity and interspecific interaction between Spartina alterniflora and Scirpus mariqueter during seed germination and vegetative growth stages by controlled environment experiments, aiming to further understand the influence of regeneration on plant community assembly of salt marshes. The major findings of this study are as follows. (1) In Petri dish germination experiment, germination rate of Spartina alterniflora seeds was not significantly affected by salinity and interspecific interaction, but the germination speed was significantly slowed down under 1% NaCl treatment. Germination rate of Scirpus mariqueter was significantly inhibited by high salinity, and the effects of interspecific interaction were regulated by salinity. Scirpus mariqueter seeds were significantly facilitated by Spartina alterniflora seeds in 1% NaCl solution, but not in fresh water. Germination speed of Scirpus mariqueter seeds was also significantly slowed down under 1% NaCl treatment, but interspecific interaction had no significant effects. (2) In interaction mechanism experiment, germination rate of Spartina alterniflora seeds was significantly promoted by Scirpus mariqueter seeds in mixture, and the germination speed was significantly slowed down in soak solution of competitor seeds. Germination rate of Scirpus mariqueter seeds was significantly promoted by Spartina alterniflora seeds, whereas the germination speed was significantly slowed down. For both species, the salinity of culture solution was significantly lower in mixture than in other treatments. Hence, the interspecific interaction between Scirpus mariqueter and Spartina alterniflora seeds was not mediated by allelopathy. The facilitation may be caused by salt absorption during the germination process. (3) In pot experiment, high salinity also inhibited Scirpus mariqueter more than Spartina alterniflora. Germination and vegetative growth (average shoot height and aboveground biomass) were generally inhibited in mixture compared with those in monoculture, but the difference was not significant. Interspecific competition was affected by stress and life history stage, which became more intense in more stressful environment and late life history stage. In newly formed salt marsh plant communities, environmental factors such as salinity play more important roles, whereas in mature communities, interspecific competition becomes the dominant factor which determines the community pattern.