Seagrass beds support vital ecological functions so that when seagrass experience severe degradation, their ecosystem service functions are diminished or lost. The largest Nanozostera japonica seagrass bed in China, situated in the Yellow River Delta, has undergone significant degradation due to Spartina alterniflora invasion and the impact of Typhoon Lekima (2019). The lack of seeds and overwintering shoots makes natural seagrass recovery challenging, prompting the urgent need for seagrass ecological restoration. In the present study, seed sowing experiments were conducted with varying burial depths, seed sources, and sowing times, as well as transplantation experiments with different transplant unit sizes and intervals in the severely degraded seagrass bed. Subsequently, changes in macrobenthos and soil bacterial diversity were tracked after seagrass recovery. According to the results, the optimal burial depth for N. japonica seeds varies across different sediment types, with 4 cm being suitable for sandy soil and 2 cm for silty soil. Seeds sown in May did not survive due to high temperatures. Seeds from Dalian exhibited superior growth after sowing, making them ideal material for seed restoration projects. Transplanting N. japonica sods with 25 × 25 cm transplant units and 50-cm intervals resulted in the most robust growth, indicating it as a suitable method for adult transplantation. Following seagrass re-establishment, macrobenthos and soil bacterial diversity increased significantly. The findings of the present study provide valuable technical guidance and theoretical support for the ecological restoration of N. japonica. Future efforts should prioritize the restoration of seagrass bed ecological functions, with longer-term effects examined.