Marine plastic pollution has become a major global environmental issue combined with global climate change, ozone depletion, and ocean acidification. Microplastics (less than 5 mm in diameter), as emergent contaminants, are of great concern globally. Available studies show that microplastics are present in marine fisheries waters, and marine fishery organisms, an important source of high-quality protein for humans, have been contaminated by microplastics. Therefore, the study on microplastics pollution in marine fishery waters and their biological effects has attracted increased attention. In the present study, we summarized the main sources of microplastics in marine fishery waters and their pollution status, summed up the main toxic effects of microplastics on the marine fishery organisms and the corresponding toxicity mechanisms, discussed the transfer of microplastics along the marine food chain and their potential impact on the quality and safety of seafood, analyzed the current problems, and finally, provided the outlook for future work. This study provides a scientific basis for better evaluation of the effect of microplastics on the marine fisheries resources as well as seafood quality and safety.