The aquaculture and fisheries sectors play critical roles in promoting a global nutritious and climate-friendly food system. The Japanese government started implementing the discharge of nuclear-contaminated water (NCW) into the Pacific Ocean in August 2023, which was followed by stopping the import of seafood from Japan to ensure the safety of imported food for Chinese citizens. The discharge of NCW into the ocean by Japan will directly harm the marine ecological environment and the global ecosystem due to the importance of China as the largest producer, processor, and exporter of aquatic products (APs). This paper employs the Global Trade Analysis Project (GTAP) model to simulate the future impacts of discharging the NCW under three different scenarios. The results showed that discharging NCW will lead to a global decline in AP production and also has negative repercussions on the macroeconomic landscape. Japan will face the most significant negative impact on its national macroeconomy, e.g., Japan’s GDP, total imports, total exports, household income, and social welfare will decrease by 2.18%, 3.84%, 8.30%, 2.61%, and $130.07 billion; similarly, for China, the decrease will be 0.03%, 1.21%, 0.08%, and $728.15 billion, respectively. If China’s AP consumption decreases by 10% and 20%, it will result in protein deficits of 1.536 million tons and 3.132 million tons, respectively. Japan’s deficit will reach 138,000 tons and 276,000 tons. This necessitates supplementation via the consumption of other protein-rich foods, posing a significant threat to the nutritional security of food in both China and Japan.