Methane (CH4) emissions from aquatic ecosystems, including wetlands, freshwater bodies, and rice paddies, contribute significantly to global warming due to CH4’s high global warming potential. Traditional CH4 mitigation strategies, such as mechanical aeration, sediment capping, and vegetation management, face challenges related to high costs, inefficiency in oxygen delivery, and ecological disturbances. In recent years, interfacial oxygen nanobubbles (IONBs) have emerged as a promising geoengineering solution for reducing CH4 emissions by providing sustained oxygenation in anoxic sediments. Unlike conventional methods, IONBs exhibit high stability, prolonged oxygen retention, and slow, controlled oxygen release, reducing the need for frequent re-application. This sustained oxygenation creates long-lasting aerobic microenvironments that suppress methanogenesis while stimulating methanotrophic CH4 oxidation. Furthermore, IONB-loaded carriers, such as biochars and zeolites, enable targeted oxygenation, improving redox conditions and promoting beneficial microbial shifts. Compared to mechanical aeration, which rapidly dissipates oxygen, or chemical amendments requiring repeated treatments, IONBs provide a low-maintenance, cost-effective alternative with minimal ecological disruption. This review explores the physicochemical properties of IONBs, their mechanisms of action in altering sedimentary biogeochemical processes, and their potential applications in mitigating CH4 flux from different aquatic ecosystems. Despite their potential, challenges remain in optimizing oxygen-loading capacity, assessing long-term ecological impacts, and scaling up production. Future research should focus on refining the oxygen-loading capacity of IONBs, integrating them with existing mitigation approaches, and evaluating their role in global climate policies. As an innovative and sustainable tool, IONBs hold great promise for advancing wetland conservation, reducing agricultural CH4 emissions, and climate change mitigation efforts.