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The climatology of circulations in South China Sea was developed on base of Princeton Ocean Model (POM) with horizontal resolution and 21 sigma-levels in vertical direction.The circulation variations were decomposed into two modes: one which was caused by local forcings and another which was acted through open boundaries.The volume transport through five key channels was discussed with the model output in combination with related literatures.The biogeochemical element (C,N,P) transport through five key channels and discharged from main rivers were calculated in orientation to estimate the basin-wide mean variation with data all available.This research set a milestone toward developing a 3-dimensional biogeochemical cycling model in South China Sea.