It is necessary to restore the declined eelgrass Zostera marina L. beds which have multiple functions. The utilization of seedlings to recover eelgrass beds can maintain the genetic eelgrass diversity; however, the seedling establishment rate that is affected by many habitat factors is very low. Manila clam Ruditapes philippinarum (Adams & Reeve, 1850) transform habitats through several ways. Thus, it is inferred that the clam affects the establishment of eelgrass seedlings in multiple ways, and the seedling establishment rate of eelgrass might not simply increase or decrease under the presence of clams. To verify this hypothesis, a five-month clam-mediated seedling establishment experiment was conducted. The contents of total nitrogen (TN) and exchangeable ammonia NH4-N (Ex-NH) in sediment increased as the clam body size increased, and TN decreased with the increase in clam abundance. There was a positive relationship between the content of organic matter in sediment (OM) and the interaction of body size and abundance of clam. The emergence rate of germinated seeds and the seedling establishment rate increased with increasing clam biomass. They were positively correlated with the interaction of OM and Ex-NH. The seedling establishment rate was negatively correlated with the interaction of water content in sediment (W) and medium diameter of sediment (Ø50), OM and TN. The presence of clams affected the height, chlorophyll b content and superoxide dismutase (SOD) activity of seedlings. The clam body size affected the SOD activity of seedlings by influencing Ex-NH. Thus, the habitat modification of clams with moderate biomass improves the establishment and traits of seedlings in multiple ways. The seedling establishment mediated by Manila clam is useful for eelgrass bed restoration.