The linkage between sea surface temperature (SST) and evaporation (EVP) plays an important role in the air-sea interaction. In this study, the interaction mechanism of SST and EVP during boreal autumn was studied using correlation analysis, composite analysis, the EVP decomposition method and singular value decomposition (SVD). The results showed that the correlation between SST and EVP in the Indian Ocean (IO) was reversed from positive to negative in the late 1990s. The significant positive SST-EVP relationship was attributed to the Indian Ocean basin mode (IOBM) forcing upon EVP during 1980–1990. The decrease in wind speed-induced EVP and SST warming led to a significant negative SST-EVP relationship during 2005–2015. Moreover, the negative SST-EVP correlation occurred when the Indian Ocean dipole (IOD) and subtropical Indian Ocean dipole (SIOD) exhibited inverse phases. The low-level moisture-EVP-SST feedback dominated the negative SST-EVP correlation in the negative IOD and positive SIOD (nIOD-pSIOD) pattern, while the wind-EVP-SST (WES) feedback played the leading role in the positive IOD and negative SIOD (pIOD-nSIOD) pattern. The EVP anomalies induced by the low-level anomalous anticyclone and cyclone were the main causes of the SST anomalies with inverse phases of the IOD and SIOD. The correlation between the SST and EVP reversal from positive to negative implies that the effect of the atmosphere on the ocean is as important as the external forcing of the ocean on the atmosphere.