We examined the distribution and seasonality of dissolved organic carbon (DOC) based on a large data set collected from the northern South China Sea (NSCS) shelf under complex circulation schemes influenced by river plume, coastal upwelling, and downwelling. The highest surface values of ∼117 μmol L−1 were observed nearshore in summer suggesting high DOC supplies from the river inputs, whereas the lowest surface values of ∼62 μmol L−1 were on the outer shelf in winter due to entrainment of DOC‐poor subsurface water under strengthened vertical mixing. While the summer coastal upwelling brought lower DOC from offshore depth to the nearshore surface, the winter coastal downwelling delivered higher surface DOC to the midshelf deep waters from the inner shelf fueled by the China Coastal Current (CCC) transporting relatively high DOC from the East China Sea to the NSCS. The intensified winter downwelling generated a cross‐shelf DOC transport of 3.1 × 1012 g C over a large shelf area, which induced a significant depression of the NSCS DOC inventory in winter relative to in autumn. In addition to the variable physical controls, net biological production of DOC was semiquantified in both the river plume (2.8 ± 3.0 μmol L−1) and coastal upwelling (3.1 ± 1.3 μmol L−1) in summer. We demonstrated that the NSCS shelf had various origins of DOC including riverine inputs, inter‐shelf transport and in situ production. Via cross‐shelf transport, the accumulated DOC would be exported to and stored in the deep ocean, suggesting that continental shelves are a potentially effective carbon sink.