Microplastics were recently found to aggregate in the blue carbon ecosystems (BCEs), which are known for their ability to store carbon by slowing down the water flow. However, evidence is largely lacking on how the accumulation of microplastics is related to carbon sequestration in BCEs and if this trap effect is driven by its biological characteristics. In this study, the trap effect of microplastics by BCEs was evaluated for various seagrasses (Zostera japonica, Halophila ovalis, and Halophila beccarii) and mangroves (Aegiceras corniculatum and Avicennia marina). Significant accumulation was found in the seagrass meadow dominated by H. beccarii and the mangrove forest dominated by A. marina, with microplastics enriched by 1.3 to 17.6 times compared to their corresponding unvegetated sites. The abundance of microplastics varied greatly from 17.68 ± 8.10 to 611.75 ± 81.52 particles per kg of dry sediment, with the highest abundance in A. marina mangrove sediments. A strong positive correlation was found between the abundance of microplastics and the particulate organic carbon content at all study sites (Pearson, R = 0.86, p < 0.01). Higher diversity of microplastic colors and size was found in the H. beccarii meadow, and higher diversity of shapes was found in the A. marina forest. Our results added new insights to the understanding of the mechanism of microplastic trapping by BCEs and coupled the behavior of microplastics with the organic carbon in the sediment.