In the present study an attempt has been made to investigate the impact of salinity stratification on the SST during the tropical cyclone (TC) passage. In this context, a severe post monsoon cyclone, Sidr, (Category 4) that developed over the south-eastern Bay of Bengal (BoB) during 11–16 November, 2007 was chosen as a case study. Pre-existence of a thick barrier layer (BL), temperature inversions and a higher effective oceanic layer for cyclogenesis (EOLC) were noticed along the path of the Sidr cyclone. The analysis of available Argo floats along the Sidr cyclone track also revealed less cooling during as well as after its passage as was reported from satellite derived SST. The role of BL on Sidr induced sea surface cooling was investigated using a diagnostic mixed layer model. Model results also depict the reduced sea surface cooling during the passage of Sidr. This is attributed to the presence of BL which results in the inhibition of the entrainment of cool thermocline water into the shallow mixed layer. Climatological as well as in situ observations of tropical cyclone heat potential (TCHP) and EOLC shows that the Sidr cyclone propagated towards the regions of higher EOLC.