More than ten years of satellite-derived net primary prodction (NPP) data were used to investigate the interannual variations of NPP associated with two different types of El Niño in the South China Sea (SCS). Results of the empirical orthogonal function analysis (EOF) show that the first two modes have significant interannual variations and are sensitive to two types of El Niño respectively. The first mode is highly correlated to the canonical El Niño. This mode is characterized by basin-scale decreased NPP during the canonical El Niño years, predominantly diminished off the east coast of Vietnam and the northwest coast of Luzon. The second mode is well correlated to the El Niño Modoki, showing increased NPP in the central and eastern SCS during the El Niño Modoki years. The interannual NPP variability is linked to anomalous atmospheric and oceanic conditions associated with these two types of El Niño. During the developing phase of El Niño Modoki, enhanced western North Pacific summer monsoon and moderate northeasterly wind divergence gave rise to the positive wind stress curl anomalies in the central and eastern SCS, inducing strong Ekman upwelling and increased upward nutrient supply. The moderate Ekman upwelling in the mature phase of El Niño Modoki also sustained the ocean primary productivity. Basin-scale decreased NPP in the SCS was attributed to anomalous weakened wind and abnormal warm sea surface temperature throughout the period of canonical El Niño.