The sustainable blue economy is crucial for coastal regions. It not only fosters economic development along the coastlines but also reduces their impact on marine environments and ecosystems. This will be a significant economic growth point for coastal areas in future decades. However, comprehensive research on assessing the blue economy is currently limited; existing evaluation methods are few and may not be applicable to all contexts. This study introduces the Blue Economy Index (BEI), a novel framework for evaluating the sustainable blue economy, and applies it in Japan's 39 coastal prefectures. Grounded in multi-dimensional analysis, the BEI includes four sectors: Ocean Resources and Marine Industry, Environmental and Ecological Sustainability, Socio-Economic Stability, and Risk Management. Utilizing Japan's prefectural data and addressing regional disparities, the index applies four weighting scenarios—Equalitarianism, Preservationist, Sustainable Use, and Extractive Use—to reflect different developmental strategies. The result indicates a significant imbalance in blue economy development across prefectures, with leading regions like Hokkaido, Tokyo, and Okinawa vastly outpacing others such as Ibaraki and Tottori. Additionally, the development status in 39 coastal prefectures in Japan demonstrates the cluster phenomenon and exhibits a '2 high, 3 middle, 1 low' development pattern, which comprises two extraordinary clusters and four distinctive clusters. We propose to implement zonal management for Japan's Exclusive Economic Zone (EEZ) and establish a National Ocean Agency. Promoting committee-based regional management, provide corresponding subsidies to enhance capacity building. Additionally, and drive the digital transformation in the marine sector through quantifiable indicators as BEI. The study underscores the necessity for improving current policy and regulation, as well as promoting inter-prefectural collaboration to boost the development of the blue economy. The BEI's comprehensive approach offers an example of global sustainable blue economy assessments. Policymakers and stakeholders in other countries can flexibly use and adjust the BEI method to conduct appropriate regional assessments and develop quantifiable strategies to improve the potential of marine sectors.