The lagging and leading correlations among satellite observations, reanalyzed biogeophysical data, and the Nino3.4 El Niño index were investigated to reveal the impacts of El Niño on the phytoplankton biomass (chlorophyll a [Chl a ]) in the South China Sea (SCS), in an attempt to identify the probable responsible factors in greater spatiotemporal detail. A basin‐scale high Chl a concentration during the developing phase of El Niño changed to basin‐scale low Chl a during the weakening phase. Cyclonic wind circulation in the northern basin, increased wind speed in the southern basin, and strengthened upwelling off the Vietnamese coast likely caused a basin‐scale nutrient increase during the developing phase of an El Niño event; the opposite conditions led to low nutrient levels during the weakening phase. Decreases in Chl a east of the Vietnamese coast and northwest of Borneo Island were due to decreases in nutrients supplied by rivers. These spatiotemporal changes are considered biogeophysical responses to a variety of types of El Niño. Regardless of the El Niño type, reanalyzing biogeophysical data sets during central Pacific warming separately from those during eastern Pacific warming is recommended for a more robust understanding of the detailed spatiotemporal impacts of different El Niño types on the biogeophysical environment of the SCS.