Degree of oxygenation in intermediate water modulates the downward transferring efficiency of primary productivity (PP) from surface water to deep water for carbon sequestration, consequently, the storage of nutrients versus the delivery and sedimentary burial fluxes of organic matter and associated biomarkers. To better decipher the PP history of the South China Sea (SCS), appreciation about the glacial-interglacial variation of the Luzon Strait (LS) throughflow, which determines the mean residence time and oxygenation of water mass in the SCS interior, is required. Based on a well-established physical model, we conducted a 3-D modeling exercise to quantify the effects of sea level drop and monsoon wind intensity on glacial circulation pattern, thus, to evaluate effects of productivity and circulation-induced oxygenation on the burial of organic matter. Under modern climatology wind conditions, a 135 m sea level drop results in a greater basin closeness and a ~ 23 % of reduction in the LS intermediate westward throughflow, consequently, an increase in the mean water residence time (from 19 to 23 year). However, when the wind intensity was doubled during glacial low, the throughflow restored largely to reach a similar residence time (18.4 years) as today regardless its closeness. Comparing with present day SCS, surface circulation pattern in glacial model exhibits (1) stronger upwellings at the west off Luzon Island and the east off Vietnam, and (2) an intensified southwestward jet current along the western boundary of the SCS basin. Superimposed hypothetically by stronger monsoon wind, the glacial SCS conditions facilitate greater primary productivity. Manganese, a redox sensitive indicator, in IMAGES core MD972142 at southeastern SCS revealed a relatively reducing environment in glacial periods. Considering the similarity in the mean water residence time between modern and glacial cases, the reducing environment of the glacial southeastern SCS was thus ascribed to a productivity-induced rather than ventilation-induced consequence.