In this study, paleoproductivity on millennial scales was precisely reconstructed from core MD12-3428cq in the northern South China Sea (SCS) over the past 24 kyr, based on a transfer function derived from the strong exponential negative correlation between relative abundance of Florisphaera profunda (%FP) in core top sediments and basin-wide satellite-based primary productivity (PP) in the SCS. To detect the potential driving mechanisms of PP, correlation analyses were carried out among our PP records and other paleoenvironment parameters. PP peaked during 18–15 ka in parallel with the strong East Asian Winter Monsoon (EAWM). From 15 ka to the early Holocene, a decrease in PP coincided with sea level progradation and weakening of EAWM, which ultimately reduced fluvial nutrient levels and wind-driven upper water column mixing. Since the middle Holocene, gradually more frequent El Niño-Southern Oscillation (ENSO) events have taken place, further decreasing PP by injecting oligotrophic Kuroshio water masses into the northern SCS. Associated findings conclusively indicated that the main controlling factors of PP in the northern SCS have shifted from EAWM (glacial) to ENSO (interglacial) over the past 24 kyr.