The Maluku Sea features strong Chlorophyll-a (Chl-a) bloom and sea surface temperature (SST) cooling during the Southeast Monsoon season. Using high-resolution Chl-a and SST satellite observations over a long time window, this study aims to investigate the effect of El Nino Southern Oscillation (ENSO) on the seasonal variability of Chl-a and SST in the Maluku Sea. During the El Nino and La Nina, the maximum Chl-a concentration (greater than 0.5 mg/m3) and minimum SST (less than 27.5 °C) are observed in August. This finding is in line with prior investigation. Moreover, we reveal that the ENSO does not alter the seasonal variability of Chl-a and SST in the region, but the magnitudes of summertime Chl-a bloom and SST cooling are enhanced (reduced) by about 0.1 mg/m3 and 0.5 °C during the El Nino (La Nina). This is caused by an increase (decrease) in the sea level pressure gradients, which possibly enhanced (reduced) wind-driven mixing in the Maluku Sea.