This study finds that the winter barrier layer (BL) in the Bay of Bengal (BoB) can modulate the subsequent Indian summer monsoon (ISM) onset and associated rainfall variability. In the years when the prior winter BL is anomalously thick, there is anomalous sea surface cooling caused by intensified latent heat flux loss, and this anomalous cooling persists into the following year due to positive cloud–SST feedback. During December–February, it is shown that the vertical entrainment of warmer subsurface water due to anomalously thick BL acts to limit excessive cooling of the sea surface and maintain deep atmospheric convection over the BoB. Then, during March–May, the thinner mixed layer linked to anomalously thick BL allows more shortwave radiation to penetrate below the mixed layer. This tends to reinforce the cold SST anomalies, and advance the onset of ISM and enhance June ISM precipitation through an increase in the tropospheric temperature gradient between land and sea. We also find that most CMIP5 models fail to reproduce the observed relationship between June ISM rainfall and the prior winter BL. This may be attributable to their difficulties in realistically simulating the winter BL in the BoB and ISM precipitation. The present results indicate that it is important to realistically capture the winter BL of the BoB in air–sea coupled models for improving the simulation and prediction of ISM.