A common but often less tested explanation for the successful invasion of alien species is that invasive alien species outcompete their co-occurring natives, which may not always be the case. In this study, we established artificial environmental gradients in a series of pot experiments with controlled environments to investigate the effects of salinity, sediment type and waterlogging on the performance of and interactions between Phragmites australis (native) and Spartina alterniflora (alien), which generally co-exist in the saline intertidal zones of Chinese and American coasts. Significant effects of salinity and waterlogging were detected on biomass production and morphological characteristics of S. alterniflora and P. australis, and the competitive interactions between the two species were found to vary with all three environmental factors in our experiments. Relative Neighbor Effect (RNE) analyses indicate that competitive dominance of S. alterniflora occurred under the conditions of high salinity, sandy sediment and full immersion, whereas P. australis showed competitive dominance under the conditions of low salinity and non-immersion. Our results suggest that S. alterniflora might outcompete P. australis under conditions present in early salt marsh succession, which support the viewpoint that the outcomes of competition between co-occurring native and invasive alien plants depend on the growing conditions. The implication of this study is that in response to the environmental changes expected from seawater intrusion and sea-level rise, the range of S. alterniflora is expected to expand further in the Yangtze River estuary in the future.