Abstract: The capability of three sets of high-resolution reanalysis datasets (GLORYS12V1, HYCOM, and BRAN2020) in depicting the 3D structure of intrathermocline eddy (ITE) is evaluated based on the complete passage process of a mesoscale intrathermocline eddy observed by a buoy in the tropical southeastern Indian Ocean. The results show that all the three reanalysis datasets can reasonably reproduce the surface anticyclonic structure of the eddy. In simulating the subsurface temperature and salinity, only GLORYS12V1 can successfully reproduce the ITE’s typical “lens-like” structure and high-salinity core features. However, none of the datasets reproduce the strong northward current with a peak velocity of 60 cm/s at the water depth of 100 m, revealing that there exist biases in simulating the subsurface flow fields. Further analysis of 3D structure based on GLORYS12V1 reveals that this eddy exhibits characteristics of high-order baroclinic modes and continuously receives a supply of equatorial water masses via geostrophic currents during its propagation, thus providing a key maintenance mechanism for its exceptionally long lifespan.