Ocean ecosystem services are fundamental to coastal economic development and climate regulation. The Tokyo Metropolitan Area (TMA) is one of the world’s most significant bay areas, with its economic development and residents relying on a healthy ocean and diverse marine ecosystem services. Post-World War II, the coastal zones of TMA have suffered from various human-induced stresses and impacts, jeopardizing the capacity of ocean ecosystem services and sustainable development. Although recent years have seen improvements in basic marine water quality, other ecosystem health issue, such as biodiversity, carbon storage, coastal protection are remain limited and require comprehensive enhancement. To better understand the current state of ocean health, promote more comprehensive ocean management decisions and plans, and support sustainable development in the region, it is essential to evaluate the ocean’s condition in the TMA and to assess future trends and risks. The Ocean Health Index (OHI) offers a comprehensive framework to evaluate global and regional ocean health conditions and their ecosystem services. This study applies the OHI to assess the ocean and coastal health of TMA, with indicators and reference points adjusted based on local conditions. From 2014 to 2019, the OHI assessment results indicate that TMA obtained an overall OHI score of 49 (out of 100), with goals ranging from 13 to 87. The environmental and social goals, such as Tourism and Recreation (87), Clean Water (67), Coastal Livelihoods and Economies (62), Sense of Place (62), and Artisanal Fishery Opportunity (51), are relatively high. In contrast, the ecological goals, such as Biodiversity (14), Carbon Storage (13), Coastal Protection (38), and Food Provision (24), are relatively low. This case study highlights strategies for improving ocean health conditions in TMA from both OHI goals and management structure perspectives. The methods and results provide a quantitative tool for regional marine and coastal management in TMA, aiding regional management organizations to establish quantifiable objectives for actions that were previously difficult to quantify. These results can indirectly promote the establishment of more comprehensive and holistic regional management organizations in TMA, which is currently fragmented, thereby effectively enhancing ocean health in TMA.