Understanding litter decomposition processes in coastal macrophyte habitats is critically important for predicting ecosystem functioning. However, decomposition processes of litter mixtures in coastal habitats remain largely unexplored. Here, we evaluated the litter mixture effects on the decomposition of six marine macrophytes (two seagrasses and four macroalgae) through in situ litter-mixing experiments with five levels of litter species richness and 36 different litter compositions. We found that the litter species identity and composition, rather than species richness, were crucial in structuring benthic faunal communities. Macroalgal litter, particularly Sargassum sp., hosted higher numbers of polychaetes and crustaceans than seagrass litter. More macroalgal presence induced faster decomposition rates of seagrass litter in the late stage, but not in the early stage. These findings suggest that changes in macrophyte diversity and composition can alter decomposition processes and, consequently, the sediment organic carbon stock through the transition of litter sources and benthic faunas.