AbstractThe barrier layer (BL) significantly impacts the upper ocean circulation and thermodynamic structure by inhibiting the heat and momentum exchange between the mixed layer (ML) and the subsurface layer. There exist sea surface temperature and salinity dipole modes in the tropical Indian Ocean, however, a BL dipole mode has not yet been identified. Using the latest observations and ocean reanalysis, here we show a robust BL dipole mode in the central and eastern equatorial Indian Ocean, which is highly correlated with the Indian Ocean Dipole (IOD) events. Composite analysis shows that the BL thickness anomalies peak in autumn and are much larger during positive IOD events than during negative IOD events. We show that a positive BL dipole phase is characterized by positive BL thickness anomalies in the central equatorial Indian Ocean and negative BL thickness anomalies in the eastern equatorial Indian Ocean, and vice versa for a negative BL dipole phase. During positive IOD events, negative surface salinity anomalies slightly affect the ML depth along the equatorial Indian Ocean. Positive subsurface temperature anomalies deepen the isothermal layer (IL) in the central equatorial Indian Ocean and strong negative subsurface temperature anomalies significantly lift the IL in the eastern equatorial Indian Ocean, controlling the BL thickness anomalies and forming a positive BL dipole pattern. This operates in an opposite direction during negative IOD events. Our study shows a close relationship between the BL dipole and the IOD and has far‐reaching implications for better understanding and predicting the IOD events.