Abstract: The combined effects of global change and human activities have led to a global decline in seagrass quality and a heightened risk of extinction. The factors regulating seagrass distribution, their dynamic patterns, and the formation mechanisms form the basis of seagrass population conservation, which is also one of the key scientific issues. In this study, we investigated the key factors affecting the potential distribution of seagrasses by integrating 13 marine environmental factors and human activity index (HAI) for two seagrass species in the Yellow Sea and Bohai Sea. The spatial and temporal distribution patterns and latitudinal trends of seagrasses in the current (2020) and future (2060 and 2100) under two climate change scenarios (SSP126 and SSP85) was predicted using MaxEnt Model and ArcGIS Pro software. The results demonstrated that the MaxEnt Model exhibited a high degree of accuracy. The primary factors driving the potential distribution of Zostera marina were human activity index, sea surface temperature (SST), slope, and nitrate concentration, with a cumulative contribution rate of 85.8%, whereas the primary factors affecting the potential distribution of Zostera japonica were water depth, slope, SST, HAI, and phosphate concentration, with a cumulative contribution rate of 87.7%. The highly suitable area of Z. marina was mainly distributed in Changshan Islands, Juehua Island, Caofeidian, Sanggou Bay, and Swan Lake, while highly suitable area of Z. japonica was mainly distributed in Changshan Islands, Miaodao Islands, and Swan Lake. In the current climatic conditions, the highly suitable areas of Z. marina and Z. japonica in the Yellow Sea and Bohai Sea were 1 006.71 km² and 838.65 km², respectively. In the SSP585 scenario, the highly suitable area of Z. marina was projected to increase by 9.68% to 1 104.14 km² by 2100. In contrast, the highly suitable area of Z. japonica was projected to decrease by 3.30% to 810.98 km² by 2100. The potential suitable areas for both seagrasses did not exhibit a discernible trend of poleward migration. There were significant conservation gaps for both seagrasses, with only 3.24% of Z. marina and 6.12% of Z. japonica were currently protected. This indicated that there was a significant conservation gap for seagrasses in the Yellow Sea and Bohai Sea, with the majority of seagrass meadows situated within mariculture zones that were subject to considerable anthropogenic activities. The establishment of scientifically planned seagrass protection areas was essential to enhance the resilience of these key ecosystems under climate change. This study provides a scientific basis for understanding the distribution patterns and degradation status of seagrasses, which is of great practical significance for targeted conservation and restoration.