We analyze the temporal and spatial variation of the thermal structure of the eastern tropical Indian Ocean associated with Indian Ocean Dipole Mode (IOD), mainly using the water temperature of 10 years (1990-1999) of the World Ocean Circulation Experiment (WOCE) repeat IX1 expendable bathythermograph (XBT) section between Java and Western Australia together with the product of the air-sea coupled four-dimensional variational analysis (4D-VAR) system. The temperature anomaly of the XBT section reveals that the change in the subsurface ocean temperature occurs earlier than that at the surface associated with IOD, i.e. the depth of the thermocline to the south of Java in years with the positive (negative) phase of IOD becomes much deeper (thinner) than the normal state before the surface IOD pattern starts to grow up. From May to August, a marked subsurface temperature anomaly is also found as well as the sea surface temperature (SST) associated with the wind anomaly along the Java coast. Heat budget analysis along IX1 shows that the surface heat flux does not dominate the mixed layer temperature anomaly near the south Java.