The seasonal and interannual variations of the barrier layer thickness (BLT) in the tropical Indian Ocean (TIO) is investigated in this study using the Simple Ocean Data Assimilation version 3 (SODA v3) ocean reanalysis dataset. Analysis of this study suggests energetic but divergent seasonal variabilities of BLT in the western TIO (5∘ N–12∘ S, 55–75∘ E) and the eastern TIO (5∘ N–12∘ S, 85–100∘ E). For instance, the thicker barrier layer (BL) is observed in the western TIO during boreal winter as a result of decreasing sea surface salinity (SSS) and deeper thermocline, which are associated with the intrusion of freshwater flux and the weakened upwelling, respectively. On the contrary, the variation of BLT in the eastern TIO mainly corresponds to the variation in thermocline depth in all seasons. The interannual variability of BLT with the Indian Ocean Dipole (IOD) and El Niño–Southern Oscillation (ENSO) is explored. During the mature phase of positive IOD events, a thinner BL in the eastern TIO is attributed to the shallower thermocline, while a thicker BL appears in the western TIO due to deeper thermocline and fresher surface water. During negative IOD events, the thicker BL only occurs in the eastern TIO, corresponding to the deeper thermocline. During ENSO events, prominent BLT patterns are observed in the western TIO corresponding to two different physical processes during the developing and decaying phase of El Niño events. During the developing phase of El Niño events, the thicker BL in the western TIO is associated with deepening thermocline induced by the westward Rossby wave. During the decaying phase of El Niño events, the thermocline is weakly deepening, while the BLT reaches its maxima induced by the decreasing SSS.