A high-resolution dinoflagellate cyst analysis on a sediment core GLW1D from the northern South China Sea (SCS) was performed to reconstruct paleoceanographic conditions over the last 12,500 years through qualitative, semi-quantitative, and quantitative methods. A modern dataset with 398 reference sites in the northern Pacific was assembled and used to identify the relationship between dinoflagellate cyst assemblages and sea-surface temperature (SST), sea-surface salinity (SSS) and primary productivity (PP). Modern analog technique (MAT) was applied to offer first dinoflagellate-cyst-based quantitative estimates of Holocene sea-surface conditions in the western North Pacific. The downcore reconstructions show that SST, SSS and PP were predominantly controlled by the changes in coastal and oceanic currents due to the changes of sea level and monsoon systems. Our results indicate that SST increased while SSS and PP decreased from 12,500 to ~6800 cal yr BP, reaching the maximum SST and the minimum SSS and PP during ~6800–5000 cal yr BP, and followed by a slight decline in SST with minor increases in SSS and PP. The three intervals correspond to the regional onshore sea-level stages of rising, stabilization in a highstand and slight drop, respectively. The Kuroshio Current strongly influenced the core site before ~9900 cal yr BP, reflected by the highest abundances of oceanic Impagidinium spp. and high reconstructed SSS values. This can be explained by a lack of water input from the East China Sea before the opening of the Taiwan Strait. The warmest period, from ~6800 cal yr BP to ~5500 cal yr BP, is recorded by the highest Dapsilidinium pastielsii abundances. Two short-term high-PP events of ~2700–2400 cal yr BP and ~1000–600 cal yr BP, which were characterized by opposite climatic conditions, coincided with two notable societal (dynasty) collapses of China. Enhanced anthropogenic activities since the Late Bronze Age most likely partially affected the high PP through influencing river inputs to the northern SCS.