Abstract The south tropical Indian Ocean (TIO) warms following a strong El Niño, affecting Indo-Pacific climate in early boreal summer. While much attention has been given to the southwest TIO where the mean thermocline is shallow, this study focuses on the subsequent warming in the southeast TIO, where the mean sea surface temperature (SST) is high and deep convection is strong in early summer. The southeast TIO warming induces an anomalous meridional circulation with descending (ascending) motion over the northeast (southeast) TIO. It further anchors a “C-shaped” surface wind anomaly pattern with easterlies (westerlies) in the northeast (southeast) TIO, causing a persistent northeast TIO warming via wind–evaporation–SST feedback. The southeast TIO warming lags the southwest TIO warming by about one season. Ocean wave dynamics play a key role in linking the southwest and southeast TIO warming. South of the equator, the El Niño–forced oceanic Rossby waves, which contribute to the southwest TIO warming, are reflected as eastward-propagating oceanic Kelvin waves along the equator on the western boundary. The Kelvin waves subsequently depress the thermocline and develop the southeast TIO warming.