In this study, the spatial and temporal variability in surface chlorophyll a (Chl-a) in the whole South China Sea (SCS) was investigated in detail by using 8-day, 4-km, gap-free MODIS-A data (2003–2016). Monthly climatology and empirical-orthogonal-functions analysis of Chl-a were performed in association with sea surface temperature and surface wind to aid in better understanding the physical mechanisms responsible for the Chl-a variability. The results are as follows: (1) Chl-a has out-of-phase variability between the coastal and open-sea regions due to different major factors controlling phytoplankton growth in each region; (2) in particular, Chl-a increases in the northern SCS during winter and in the western and southwestern SCS during summer mainly due to the effects of monsoons and orography; and (3) wind-driven coastal upwelling is stronger in the western SCS than in the eastern SCS. A wind-induced coastal upwelling not reported in the literature was detected along Palawan Island (8–12∘N, 117–120∘E) during winter. In the SCS, the Chl-a variability is influenced by the El Nino–Southern Oscillation with a time lag of 4–9 months, depending on the variability scales.