The environmental behavior of microplastics (MPs) in estuaries with saline and freshwater intersections is extremely complex. This increases the chance of MP ingestion by fishery resources, posing potentially tremendous health risks for humans. Herein, a total of 105 fishes from 14 different species, and 86 crustaceans (including shrimps and crabs) from five different species were sampled in the Yangtze River estuary and offshore, and MP bioaccumulation, accumulative organ, and the influencing factors were comprehensively studied. The results elucidated that MP accumulation in benthos was significantly higher than that in pelagic animals due to the lower acceptance threshold, assimilation efficiency and egestion rate for benthos. The MP content in crustaceans with the burrowing favoring the MP retention was significantly higher than that in fishes. MPs ingested by fish can accumulate in skin, gills and viscera rather than muscles. Most MPs accumulated in fishery resources were cellulose and polyethylene terephthalate characterized by black and gray fibrous and lengths ranging from 0.1 mm to 1 mm. The gill retention capacity of pelagic fish to smaller-size (<0.1 mm) MPs was pronouncedly stronger than that of benthic fish. It was more accurate to assess the ecological risk of MPs in terms of the maximum size of MPs accumulated in organisms. Compared with the offshore area, the incidence of MP uptake was higher in the estuary owing to anthropogenic impacts. This study helps understand the transfer of MPs in aquatic food webs and offers a foundation for assessing the risk of human exposure to MPs.