The integration of green manure (GM) crops into traditional cropping systems has regained attention for its potential to improve soil organic carbon (SOC) content in an environmentally sustainable way. However, the effects of carbon (C) input from different GM species on the SOC accumulation and recalcitrant C fractions across soil profile remain inadequately understood. This three-year field study in the North China Plain assessed SOC changes and C fractions of easily oxidizable carbon (EOC) and recalcitrant organic carbon (ROC) in fallow, rye, rapeseed, and vetch systems, with δ¹³C analysis for GM-derived C fraction and microbial C-decomposition functional genes. Our results showed that SOC was significantly increased by GMs. Rapeseed was the only species that improved SOC at 20–40 cm, the rapeseed-derived C contributed 2.48% of the SOC. Rye enhanced EOC and ROC at topsoil, rapeseed increased ROC at 20–60 cm, and vetch increased EOC at 40–60 cm. At the topsoil, the abundances of cellulose- and pectin-decomposition genes were increased in vetch and decreased in rye. At 20–40 cm, the pectin- and lignin-decomposition genes were markedly improved by rapeseed, while at 40–60 cm, the chitin-decomposition gene was increased in vetch, indicating the microbial promoting effects by deep roots of vetch and rapeseed. Our results suggest GM species influence SOC deposition depth and the recalcitrance of SOC decomposition, thereby affecting the distribution of SOC accumulation through microbial-driven C decomposition activities.