The South China Sea (SCS) is one of the largest marginal seas in the world and it plays an important role in regional climate change and carbon cycles. However, mechanisms of glacial–interglacial phytoplankton productivity changes remain under-studied, especially for the southeastern SCS. In this study, the productivity record for the southeastern SCS (core MD972142) over the last 185kyr was generated using multiple biomarkers, including C37 alkenones (C37:2+C37:3), brassicasterol, dinosterol, and alkyl diols (C30+C32) as productivity proxies for haptophytes, diatoms, dinoflagellates, and eustigmatophytes (and diatoms), respectively. All biomarker contents indicate higher individual as well as total phytoplankton productivities during peak glacials than during interglacials. Our records afford a better constraint on spatial pattern of glacial productivity changes, which suggest that both the southeastern and northern SCS glacial productivity increases were controlled by the stronger East Asian winter monsoon (EAWM), which brought more nutrients to the surface through stronger mixing of nutrient-rich deep waters. Biomarker ratios reveal a relatively stable phytoplankton community structure (PCS), but relative diatom productivity was higher during glacials. The PCS record is consistent with stronger EAWM forcing during glacials, which supplied nutrients to the surface with relatively stable composition. The decrease of C37 alkenones during the last 120kyr is likely a global phenomenon, which could be related to the evolution of the haptophytes. In the SCS, this trend was also likely caused by changes of subsurface nutrient supply to the SCS, which significantly modulated the PCS by a gradual decrease of haptophyte contribution to total phytoplankton in the northern and southeastern SCS since MIS 5.