Microplastic pollution of intertidal mangrove ecosystems is receiving growing attention, and scientists suspect that the microplastic pollution of semi-enclosed seas is significantly different from that of other coastal types because of their unique geographical features. However, data on the distributions and characteristics of microplastics in the mangrove sediment of semi-enclosed seas are very limited. This study selected the Maowei Sea, a typical semi-enclosed sea, as its representative study site. The analysis revealed that the microplastic abundances in the river estuaries were much lower than those at the oceanic entrance zones, with values ranging from 520 ± 8 to 940 ± 17 items/kg. Polyethylene (PE)/polypropylene (PP)/polystyrene (PS), white/transparent, and <1 mm were the dominant type, colour, and size of the microplastics, respectively, in the observed mangrove sediments. Moreover, some other factors, including the rhizosphere/non-rhizosphere and the proportion of organic matter, codetermined the distribution and characteristics of microplastics. Specifically: (1) the percentage of colorful microplastics were higher in the rhizosphere due to the microbial activities and (2) positive linear relationships were found between the pore volume (PV) values of the free particulate organic matter (FPOM), occluded particulate organic matter (OPOM) (1.6–2.0 g/cm3 and >2.0 g/cm3), and the abundance of very small microplastics (<1 mm). Display omitted •Microplastics were first detected in the mangrove sediment of the semi-enclosed sea.•Factors determining microplastic contents in estuaries and entrances differed.•Pore structure influenced the microplastic content in mangrove sediment.•Microbial activity in rhizosphere accelerated the microplastics' colour changes.