The El Niño event is a major large-scale air-sea interaction phenomenon over the tropical Pacific region. Previous studies classified El Niño into three types — canonical El Niño, El Niño Modoki I, and El Niño Modoki II. This research reveals that different types of El Niño present dramatic effects on the interannual variability of sea surface salinity over the central equatorial Indian Ocean in the boreal autumn. The decreasing (increasing) sea surface salinity during the canonical El Niño and the EI Niño Modoki I (the EI Niño Modoki II) events is identified. The salinity budget analysis is performed to identify the dominant factors responsible for the variability of sea surface salinity over the central Indian Ocean. The results indicate that the wind-driven anomalous zonal advection plays an important role in sea surface salinity variability during the El Niño events associated with the forcing from the anomalous Walker circulation over the equatorial Indian Ocean.