Circadian POC-diurnal and nocturnal cycling of particulate organic carbon (POC)- could influence their seasonal and interannual biogeochemical patterns. In order to understand circadian POC in oligotrophic northern South China Sea, this study conducted a continuous 24 h time-series sampling across four depths (5 m, chlorophyll maximum depth, 200 m, and 662 m) of one site on the continental slope and analyzed optical properties of suspended particulate matter (SPM), POC properties, microbial community abundance and respiration rate (MCR) of size-fractionated microorganisms, and their dark carbon fixation rates (DCF). The results suggested varying degrees of coupling among SPM, POC, MCR, microbial abundance, and light intensity, associated with different primary production and diel vertical migration patterns. Size-fractionated analysis revealed three distinct metabolic patterns but no significant differences in their contribution to total MCR: synchronized variations between abundance of small phytoplankton and bacterioplankton organisms (0.2–0.8 μm) followed a “fast carbon cycling mode”; medium organisms (0.8–3.0 μm) showed significant correlations between bacterial abundance, POC, and MCR, functioning as primary POC decomposers; and large organisms (>3.0 μm) displayed decoupled metabolic patterns, potentially utilizing non-primary productivity carbon sources. Dark carbon fixation (56.9 ± 9.2 mg C m⁻² d^-1) was an important POC supply besides export production and lateral transport in the deep ocean. The study emphasized the critical importance of considering the science of circadian POC when assessing biological carbon pump efficiency in oligotrophic marginal seas.