Marine transgressions-regressions have profoundly shaped marginal seas following global sea-level fluctuations driven by climate change. This study on a sedimentary core profile SO219/31-4 from the Beibu Gulf, northwestern South China Sea (SCS), reveals information about paleoenvironment, paleoceanography and paleoclimate changes through fossil diatom assemblages and grain size distributions during the last ca. 12900 cal. yr. BP. Eight local diatom assemblage zones were distinguished and assigned to paleoenvironmental fluctuations recording sea-level and depositional environment changes in eight stages, ca. 12900–11700 (stage 1), ca. 11700–9500 (stage 2), ca. 9500–7200 (stage 3), ca. 7200–5800 (stage 4), ca. 5800–3800 (stage 5), ca. 3800–2400 (stage 6), ca. 2400–800 (stage 7) and ca. 800–0 (stage 8), cal. yr. BP. After the low sea level of stage 1 within the last deglaciation, rapid increases in sea level in stages 2 and 3 were recorded as meltwater events pulse-1B and pulse-1C resulting in marine transgression rates of ca. 16 m/kyr and 8 m/kyr, respectively. The high sea level, above the present level, in stages 4 and 5, in the Middle Holocene Climatic Optimum period, was clearly documented by more significant open sea/tropical diatom species and coastal planktonic species percentages, respectively. The late Holocene regression of sea levels was marked by a pronounced reversion of diatom taphocoenosis, responding to neoglacial climate. Fossil diatom assemblages outlined responded to paleoclimate of global warming in the deglacial and early Holocene. This study provides additional insights into the late Pleistocene and Post-glacial history of a tropical-subtropical shallow water gulf, in the NW-SCS.