Microplastics (MPs) contamination in marine environment has been an emerging issue worldwide, notably due to the potential ecological risks of MPs with co-existing environmental contaminants and released toxic plastic additives. To verify the co-occurrence characteristics of MPs and co-existing pollutants in the benthic boundary layer (BBL), the distribution characteristics of MPs, and selected heavy metals (HMs) and halogenated flame retardants (Polybrominated diphenyl ethers, PBDEs, and Dechlorane Plus) in the bottom water and sediment were comprehensively investigated in the East China Sea (ECS). The sampling sites were selected along the coast of ECS, where might be significantly affected by terrigenous inputs and anthropogenic sources. MPs were abundant in the bottom water (62.8–480.2 items/L) and sediment (80.1–1346.7 items/kg d.w.) with polyester, polyethylene, and polypropylene being as the most abundant types and characterized as fiber/line, particle size 200–500 μm, and transparent/white. The abundance and characteristics of MPs demonstrated strong correlations within the bottom water and sediment, which might be due to the frequent exchange of materials. In addition, the abundance of MPs was significantly positively correlated with HMs (Cd, Cr, Pb) in the bottom water and PBDEs in sediment, respectively. According to the scanning electron microscopy/energy dispersive X-ray spectrometry analysis, MPs might act as carriers to transport and co-sediment the co-existing pollutants in water, and physically adsorb or chemically bind with pollutants in sediment. These results could help to elucidate the sources, migration, and fate, and verify the occurrence and potential risks of MPs and their co-existing pollutants in BBL, thus realize the management and control of MPs contamination in marine.