Sea surface height derived from the multiple ocean satellite altimeter missions (TOPEX/Poseidon, Jason-1, ERS, Envisat et al.) and sea surface temperature from National Centers for Environmental Prediction (NCEP) over 1993–2008 are analyzed to investigate the coherent patterns between the interannual variability of the sea surface and subsurface in the Tropical Indian Ocean, by jointly adopting Singular Value Decomposition (SVD) and Extended Associate Pattern Analysis (EAPA) methods. Results show that there are two dominant coherent modes with the nearly same main period of about 3–5 yr, accounting for 86 % of the total covariance in all, but 90° phase difference between them. The primary pattern is characterized by a east-west dipole mode associated with the mature phase of ENSO, and the second presents a sandwich mode having one sign anomalies along Sumatra-Java coast and northeast of Madagascar, whilst an opposite sign between the two regions. The robust correlations of the sea surface height anomaly (SSHA) with sea surface temperature anomaly (SSTA) in the leading modes indicate a strong interaction between them, though the highest correlation coefficient appears with a time lag. And there may be some physical significance with respect to ocean dynamics implied in SSHA variability. Analyzing results show that the features of oceanic waves with basin scale, of which the Rossby wave is prominent, are apparent in the dominant modes. It is further demonstrated from the EAPA that the equatorial eastward Kelvin wave and off-equatorial westward Rossby wave as well as their reflection in the east and west boundary, respectively, are important dynamic mechanisms in the evolution of the two leading coherent patterns. Results of the present study suggest that the upper ocean thermal variations on the timescale of interannual coherent with the ocean dynamics in spatial structure and temporal evolution are mainly attributed to the ocean waves.