Ecological corridors are crucial pathways for wildlife migration, dispersal, and life cycle completion. The spotted seal is the flagship species of three national parks strategically located in the Bohai Sea and Yellow Sea Marine Island Ecological Geographic Region (BYME). Identifying ecological corridors for spotted seals is urgent to improve conservation planning and management measures for marine spaces in relevant national parks and reduce their potential risk of local extinction. We conducted satellite beacon tracking surveys from 2010 to 2020, a participatory geographic information system (PGIS) survey on Changdao in 2023, identified BYME’s ecological corridors using niche models and Linkage Mapper, and further refined ecological corridors within the Bohai Strait based on hydrological analysis. Our results showed that there were historical records of spotted seal activity in both large-scale and small-scale ecological corridors. The large-scale corridor aligned with their crucial seasonal migration route while the small-scale corridor corresponded their habitat and feeding activity patterns. However, these corridors were not covered by existing national marine protected areas. At a large scale, shipping hotspots such as Laotieshan Waterway and Changshan Waterway block the corridor within the Bohai Strait while some key small-scale corridors may also be affected by mariculture zones. This study proposes the establishment of seasonal core zones and peripheral conservation zones in potential national parks, based on the spatial and temporal distribution of ecological corridors, while implementing dynamic management strategies aligned with migration and activity regulations.