The oxygen (δ18O) and carbon (δ13C) isotopic compositions of benthic foraminifer Cibicidoides wuellerstorfi as reliable proxies of deep water properties were compiled from 50 core‐top and down‐core sites in the South China Sea (SCS) for two time slices of the late Holocene and Last Glacial Maximum (LGM) to reconstruct the glacial deep hydrographic structure. The bathymetric profiles of both δ18O and δ13C in the SCS show similar trends between the LGM and the late Holocene, but the δ18O gradients between intermediate (∼500‐1000 m) and deep (>1500 m) waters obviously increased during the LGM, indicating an intensified bathyal stratification and weakened vertical mixing between intermediate and deep waters in the SCS during the glacial period. A spatial comparison of bathymetric δ18O and δ13C profiles was also made for the Southern Ocean (Indo‐Pacific sector) and southwest Pacific, western equatorial Pacific (i.e. Ontong Java Plateau), off‐Japan margin as well as the SCS. The meridional δ13C profiles indicate a decreasing trend of δ13C (“aging effect”) in the deep layer (∼1200‐2600 m) from south to north, reflecting a northward flow pathway of deep waters from the southwest Pacific (upstream) to the low‐latitude northwest Pacific and the SCS (downstream) during the LGM. The gradients of deep water δ18O (∼1200‐2600 m) between these upstream and downstream regions were higher during the LGM relative to the Holocene, implying that a greater contribution of the northern‐sourced North Pacific Intermediate Water (NPIW) with a relatively low δ18O signature to the deep waters in the low‐latitude Pacific during the LGM.