Microplastics (MPs), widely detected in marine environments worldwide, have emerged as a new class of pollutants that pose a major threat to the stability of marine ecosystems and the security of fisheries. MPs can accumulate in marine organisms through ingestion, gill filtration, and trophic transfer, thereby directly compromising the edible quality of marine seafood. Although several reviews have addressed the potential health risks to humans associated with MPs accumulation in seafood, systematic analyses of how MPs affect the nutritional value and flavor quality of marine aquatic products are still lacking. This study comprehensively elucidates the major sources of MPs in marine environments and their bioaccumulation routes, and focuses on the mechanisms by which MPs affect key nutritional components (proteins, fatty acids, and vitamins) of aquatic products through the core pathway of “oxidative stress–energy redistribution–gut microbiota dysbiosis”. Furthermore, from the perspectives of exogenous off-flavor introduction, endogenous metabolic disorder, and physiological imbalance of organisms, this review reveals the potential routes through which MPs cause the deterioration of flavor characteristics in seafood. These processes synergistically lead to a decline in both nutritional value and flavor quality, ultimately reducing the market value of marine products. Finally, future research directions are proposed regarding quality and safety standards and prevention and control technologies for MPs contamination in marine aquatic products. This study aims to provide theoretical support for the development of effective MPs risk prevention strategies and to promote the sustainable development of the “blue granary.”