Wetlands have degraded dramatically in recent decades due to wetland drainage, agricultural reclamation, and soil salinization in China. Soil seed banks, as a way of natural regeneration, can efficiently restore the aboveground vegetation if seeds can survive after farming. To explore the response of soil seed bank to farming and consequent environmental changes, we compared the structure and composition of soil seed banks between Carex-dominated and Phragmites-dominated natural wetlands and their adjacent farmed fields in the Songnen Plain, China. We found that the responses of soil seed banks to farming and saline-alkaline stress were different between the two community types. The seed density and species richness in Carex-dominated natural wetlands were significantly higher than nearby farmed fields, however, there was no significant difference between Phragmites-dominated natural wetlands and nearby farmed fields. Carex schmidtii and Phragmites australis, dominated in natural wetlands, were both missing after farming. At the same time, the invasive species Typha angustifolia dominated in the farmed fields. Redundancy analysis identified that soil salt content was one of the major factors which significantly affected seed bank composition. Saline-alkaline stress significantly restricted the seed germination in farmed Carex fields, however, it had no significant effect in farmed Phragmites fields. Our study indicated that the potential of vegetation restoration was restricted by seed limit and soil salinization, and it differed significantly between the original community types in the Songnen Plain. In addition to hydrological connection, special technologies (such as planting and seeding) and the improvement of soil conditions are also necessary for successful restoration in salt-affected wetlands.