Based on the temperature and salinity grid data of SODA from1980 to 2015 and combined with Argo data, the formation mechanism and seasonal variability of the barrier layer thickness in the Bay of Bengal in Indian Ocean Dipole (IOD) events are revealed. The results show that the barrier layer changed significantly in the IOD event year. In the peak of pure IOD events (pIOD) and the pIOD+El Niño events (September−November), except for the 5 m thickening of the barrier layer in the southwest of the Bay of Bengal, the barrier layer become thinner range from 5 m to 15 m in the equatorial region and the region from Andaman Sea to the northern Bay of Bengal. This form disappears as the pIOD weakens. However, the form is maintained until March to May of the following year in the pIOD+El Niño events. The variation of barrier layer in the nIOD year is roughly opposite to that of the pIOD year. Further analysis shows that the change of isothermal layer caused by the remote forcing of the equatorial wind anomaly in the IOD event is the main cause of the variability of barrier layer. In the IOD+ENSO events, the equatorial wind anomaly is maintained for more than three months after the IOD disappear, making the anomaly of barrier layer last longer in the Bay of Bengal. In addition to the equatorial forcing, the Ekman pumping in the Bay of Bengal and the variability of the salt of mixed layer also have an effect on the interannual variation of the barrier layer thickness.