Cores of marine site GeoB16602 (18.95°N, 113.71°E, water depth, 953 m) were recovered during the 2012 RV SONNE cruise SO-221 “INVERS”, northern South China Sea. Pollen samples were processed via standard hydrochloric-hydrofluoric acid procedure. Pollen and spore percentages were calculated based on the pollen sum (>300 grains per sample) and spore sum (>100 grains) respectively. The data set cover the whole last glacial cycle (140 kyr) with an average temporal resolution of ~600 years, revealing vegetation evolution history of the Pearl River catchment area in southern China. In general, the results reveal three different evolution patterns of vegetation at the tropical-subtropical flora ecotone: the zonal forest exhibited a clear glacial-interglacial cycle and weak response to stadial cooling; the fern communities exhibited similar glacial-interglacial variations but more sensitivity to low-amplitude temperature fluctuations; the glacial-interglacial trend in coastal wetland vegetation was ambiguous whereas a series of millennial-scale expansion events were closely related with sea-level rises.