Although seagrass meadows play a key role in ecosystem services by providing high productivity, their distribution areas have been declining sharply, resulting from global climate change and increased human pressures. Therefore, it is urgent to strengthen the protection and restoration for seagrasses. In this study, we tried to use seed planting method to recover the Enhalus acoroides meadow in Li’an Lagoon. Results showed that the burial depth and mesh bag protection profoundly affected the seed germination. When the burial depth was 6 cm, seed germination was very low, at 1.25%. Seeds buried in 2-cm depth with mesh bag protection showed a much higher seedling establishment (96.10%) than the seeds without protection (5.88%) in the first month, indicating that seed loss negatively affected the seed germination rate. The survival of seedlings decreased to 24.4% after three months, probably due to macroalgal blooms in the early spring.