Milkfish aquaculture plays an important role in the Philippines, as it provides food security, rural income sources, and coastal economy boosters. However, the industry is encountering several sustainability issues related to habitat destruction, pollution, resource wastage, and social injustices. This paper seeks to explore how the systems thinking approach can respond to such intertwined challenges and facilitate marine sustainability and economic resilience. Using a documentary analysis, this study analyzes environmental, economic, and social aspects of milkfish aquaculture by examining national statistics, policy papers, and scholarly literature. Based on the concepts of systems thinking and circular economy, the research traces the value chain of the industry and identifies the leverage points through which it could be intervened. The results indicate that it is necessary to combine waste valorization solutions with technological advances, which should include biofloc systems, cooperation with stakeholders, and alignment of policies with international standards. One of the proposed circular economy models shows how sustainability results can be enhanced through the production-to-consumption chain. This study concludes that applying systems thinking in milkfish aquaculture enables the preservation of marine ecosystems, promotes inclusive growth, and supports a sustainable blue economy in the Philippines.