To elucidate the seed-seedling conflict and the process of habitat choices during the expansion of S. alterniflora, densities of seeds and seedlings in three different habitats, foreland, Spartina meadow, and canopy gap patch, were measured. Statistical analyses of these measurements were performed to investigate the interaction between seeds or seedlings and environmental factors. Also, the process of habitat choice during the expansion of S. alterniflora was explored. The results show that, in the upper soil seed bank (0-5 cm), both the ratio of germinated seeds and the ratio of survival seedlings to total seeds do not differ significantly among the three habitats. However, in the lower soil seed bank (5-10 cm), these ratios differ significantly, suggesting the seed-seedling conflict of S. alterniflora generally occurs in the lower soil seed bank. The remarkable conflict occurs in the meadow habitat. Greenhouse experiments indicate that the germination rate decreases significantly and the mortality of pre-emerged seedlings increases significantly with increasing burial depth. The maximal burial depth of emerged seedlings varies with sediment types. Comparisons of burial depth effects on seedling height, mesocotyl length, coleoptile length, and root length show that the major responses of S. alterniflora preemerged seedlings to the burial treatments are the elongation of coleoptiles and mesocotyls, which favor seedling survival by enhancing aeration and accelerating emergence. These results suggest that burial treatment is a key selection factor, which leads to the seed-seedling conflict in recruitment of S. alterniflora population, and directly affects the expansion rate and the area infected by Salterniflora.