Coastal wetlands are critical components of blue carbon ecosystems, yet the functional roles of benthic shellfish species in regulating sediment carbon dynamics are not yet fully elucidated. To address this knowledge gap, we investigated the effects of different shellfish zones—gastropods (Bullacta exarata, Umbonium thomasi) and bivalves (Mactra veneriformis, Meretrix meretrix, Potamocorbula laevis)—on sediment carbon fractions and microbial communities in representative intertidal wetlands of Liaodong Bay, China. We analyzed dissolved organic carbon (DOC), particulate organic carbon (POC), microbial biomass carbon (MBC), enzyme activities, and microbial genomic profiles, with particular emphasis on carbon fixation gene abundance within the top 0–10 cm of sediment. The results showed that POC and MBC levels in gastropod zones were 56.11% and 99.83% higher, respectively, than in bivalve zones, while carbon fixation gene abundance was 14.54% lower. Structural equation modeling (SEM) further revealed that shellfish type had a significant direct effect on MBC (λ = 0.824, p < 0.001). This study provides novel evidence that shellfish community composition regulates blue carbon storage through both biogeochemical and microbial pathways, highlighting the importance of species-specific management in shellfish aquaculture to enhance carbon sequestration. These findings offer a theoretical foundation for future assessments of coastal wetland carbon sinks and ecosystem service valuation.