Soil seed banks are sources for the future regeneration of plants and play an important role in long-term population balance. Groundwater level is one of the dominant environmental factors that affects the structure and function of wetland ecosystem. While the effects and mechanisms of groundwater level on the characteristics of soil seed banks in coastal wetlands have received less attention. In order to study the effects of groundwater level on soil seed bank density, species diversity and similarity between seed banks and aboveground vegetation, a field control experiment for groundwater level was carried out following the gradients of -20 cm, -60 cm, and -100 cm in the coastal wetlands of the Yellow River Delta. The relationship between soil chemical properties and characteristics of the corresponding seed banks was analyzed by correlation analysis, principal component analysis and path analysis to explore how different groundwater levels affect the characteristics of the soil seed banks. The study showed that Suaeda glauca and Suaeda salsa had the largest number of seeds in the soil seed banks collected in autumn (both transient and persistent seed banks) in coastal saline wetland of the Yellow River Delta. The change of groundwater level had no significant effects on the density of soil seed banks, but it had significant effects on species composition. As the depth of groundwater level increased, the species number of perennial herbs were increasing. Overall, as the depth of groundwater level increased, Margalef index and Shannon-Wiener index of soil seed banks increased accordingly. A novelty finding is that the similarity (Sørensen index) between seed banks and above-ground vegetation increased as the groundwater level increased in 5-10 cm soil layer. Principal component analysis showed that soil salt including total water-soluble salt content and saline ions concentration was the dominant factors affecting soil seed bank characteristics with a contribution ratio of 69.482% and soil nutrients including total carbon, nitrogen and phosphorus concentration were the secondary factors with a contribution ratio of 23.710%. Path analysis showed that soil total water-soluble salt content had the greatest negative influence on Margalef index and Shannon-Wiener index of seed banks. While soil available phosphorus concentration showed indirectly negative effects through total water-soluble salt content on Margalef index and Shannon-Wiener index of seed banks. Total phosphorus concentration promotes the similarity between seed banks and the above-ground vegetation. Our results indicated that groundwater level fluctuation mainly affected species diversity of soil seed banks by changing the content of soil total water-soluble salt in coastal wetlands of the Yellow River Delta.