This study analyzes Indonesia’s legal construction in integrating the authority of the flag state and port state to address transnational maritime crimes within the framework of UNCLOS. As the world’s largest archipelagic state, Indonesia faces persistent threats such as drug trafficking, human smuggling, and maritime terrorism, which exploit jurisdictional gaps and fragmented institutional authority. Using a normative–prescriptive legal method, this research applies statutory analysis, conceptual interpretation, and comparative studies of maritime governance practices in Singapore, Australia, and the Netherlands. The findings reveal that although Law No. 17 of 2008 on Shipping provides a legal basis for flag state and port state functions, their implementation remains fragmented, resulting in enforcement gaps and limited functional sovereignty. This study proposes an “Integrated Flag–Port State Functional Sovereignty Model” that harmonizes national regulations, strengthens multi-agency coordination under Bakamla as a maritime fusion authority, utilizes AI-based maritime intelligence for real-time surveillance, and enhances regional cooperation through ASEAN and the Tokyo MoU. The novelty of this research lies in formulating an operational-prescriptive model that explicitly integrates flag state and port state authorities into a unified functional sovereignty framework, offering a concrete legal blueprint to improve maritime law enforcement and close jurisdictional gaps in Indonesia’s maritime governance system. Penelitian ini menganalisis konstruksi hukum Indonesia dalam mengintegrasikan kewenangan flag state dan port state guna menanggulangi kejahatan maritim transnasional berdasarkan kerangka UNCLOS. Sebagai negara kepulauan terbesar, Indonesia menghadapi ancaman serius berupa penyelundupan narkotika, perdagangan manusia, dan terorisme maritim yang memanfaatkan celah yurisdiksi serta fragmentasi kewenangan antarinstansi. Penelitian ini menggunakan metode yuridis normatif bersifat preskriptif melalui analisis peraturan perundang-undangan, pendekatan konseptual, serta studi komparatif terhadap praktik tata kelola maritim di Singapura, Australia, dan Belanda. Hasil penelitian menunjukkan bahwa meskipun Undang-Undang Nomor 17 Tahun 2008 tentang Pelayaran telah mengatur fungsi flag state dan port state, pelaksanaannya masih berjalan parsial sehingga melemahkan kedaulatan fungsional dan efektivitas penegakan hukum maritim. Penelitian ini menawarkan “Model Kedaulatan Fungsional Terintegrasi Flag State–Port State” yang menekankan harmonisasi regulasi nasional, penguatan koordinasi multi-agensi dengan Bakamla sebagai maritime fusion authority, pemanfaatan intelijen maritim berbasis kecerdasan buatan untuk pengawasan real-time, serta peningkatan kerja sama regional melalui ASEAN dan Tokyo MoU. Kebaruan penelitian ini terletak pada perumusan model integratif yang menyatukan kewenangan flag state dan port state dalam satu kerangka operasional-preskriptif guna menutup celah yurisdiksi dan memperkuat penegakan hukum maritim Indonesia.