The coast of the Yellow Sea in China, like many other temperate coastal zones, has been experiencing a dramatic decline in the abundance of seagrass. Intensive efforts have been made to restore seagrass communities along the coast to restore the function of the coastal ecosystem. Transplanting adult Zostera marina shoots is labor-intensive, time-consuming, expensive, and detrimental to donor beds; thus, restoring seagrass communities through the use of seeds is highly valued in current, large-scale restoration trials. In this study, an effective method for collecting, processing, and storing Z. marina seeds was developed. From 2009 to 2013, respectively, 122,000, 421,000, 364,000, 1,041,000, and 1,091,000 seeds were successfully collected. Two-way analysis of variance (ANOVA) showed the interaction between salinity and temperature significantly affected the cumulative germination rate (CGR) (p < 0.01) during the storage period and the viability (p < 0.01) of seeds after storage. The germination rate after storage was significantly affected by salinity and temperature (p < 0.01). The highest viability (89.8 ± 1.0%) and germination rate (75.6 ± 4.5%) were found among seeds stored at 4 ∘ C and a salinity of 44.5 psu for 7 months. The cost for planting 1 ha of sea bottom with Z. marina seeds ranged from $2,613 to $80,900 depending on the seeding density and seed loss during storage. The average cost per Z. marina seed in this study was $0.00586.