El Niño typically induces cooling in the Southwest Pacific Ocean during austral summers, usually leading to decreased marine heatwave frequency and severity. However, the 2016 extreme El Niño unexpectedly coincided with the longest and most extensive marine heatwave ever recorded in the region. This heatwave, spanning over 1.7 million square kilometers, persisting for 24 days with a peak intensity of 1.5°C, resulted in massive coral bleaching and fish mortality. This exceptional warming resulted from anomalously strong shortwave radiation and reduced heat loss via latent heat fluxes, owing to low wind speed and increased air humidity. These anomalies are attributed to a rare combined event “Madden-Julian Oscillation and extreme El Niño.” Following 10 February, the rapid dissipation of this marine heatwave results from the most intense cyclone ever recorded in the South Pacific. The hazardous ecological impacts of this extreme event highlight the needs for improving our understanding of marine heatwave–driving mechanisms that may result in better seasonal predictions.