We detected a robust cyclonic eddy in the northeastern Natuna Island in the Northwest Monsoon during an extremely negative El Niño-Southern Oscillation (ENSO) period (i.e., extreme La Niña event) using the Copernicus Marine Environment Monitoring Service (CMEMS) reanalysis results. In the intense La Niña event from 1999 to 2001, we also found an increase in the abundance of chlorophyll coincided with the eddy strength pattern using the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) data. Furthermore, this chlorophyll intensity may be related to the upwelling of water mass to the surface at the eddy’s center. The intensification of chlorophyll compared to the average value at the corresponding year is 83,4% (1999), 37.8% (2000), 37.3% (2008), and 72.5% (2011). In this paper, we revisit the identification of solid eddies in extreme La Niña events from 1999 to 2012 and further discuss the mechanism of the relationship between chlorophyll intensity and eddy strength, especially during the months of the extreme La Niña event.