The　two　key　mechanisms　for　biologically　driven　carbon　sequestration　in　oceans　are　the　biological　pump　(BP)　and　the　microbial　carbon　pump　(MCP);　the　latter　is　scarcely　simulated　and　quantified　in　the　China　seas.　In　this　study,　we　developed　a　coupled　physical-ecosystem　model　with　major　MCP　processes　in　the　South　China　Sea　(SCS).　The　model　estimated　a　SCS-averaged　MCP　rate　of　1.55　mg　C　m−2　d−1,　with　an　MCP-to-BP　ratio　of　1:6.08　when　considering　the　BP　at　a　depth　of　1000　m.　Moreover,　the　ecosystem　responses　were　projected　in　two　representative　global　warming　scenarios　where　the　sea　surface　temperature　increased　by　2　and　4°C.　The　projection　suggested　a　declined　productivity　associated　with　the　increased　near-surface　stratification　and　decreased　nutrient　supply,　which　leads　to　a　reduction　in　diatom　biomass　and　consequently　the　suppression　of　the　BP.　However,　the　relative　ratio　of　picophytoplankton　increased,　inducing　a　higher　microbial　activity　and　a　nonlinear　response　of　MCP　to　the　increase　in　temperature.　On　average,　the　ratio　of　MCP-to-BP　at　a　1000-m　depth　increased　to　1:5.95　with　surface　warming　of　4°C,　indicating　the　higher　impact　of　MCP　in　future　ocean　carbon　sequestration.　©　2018,　Science　China　Press　and　Springer-Verlag　GmbH　Germany,　part　of　Springer　Nature.