This study provides comprehensive analysis on the contrasting effects caused by the 1997 and 2015 historical El Niño events linked with the Indian Summer Monsoon (ISM) rainfall. The presence of strong southeast-northwest oriented cold Sea Surface Temperature (SST) anomalies during 1997, that spatially extended from southwest Pacific to Southeast Indian Ocean (SEIO) in comparison to the 2015 event is the robust feature. Evidently, these anomalies are closely related to interaction between cyclonic (anticyclonic) circulation over South Pacific Convergence Zone (south Australia). During 2015, the conjunction of Modoki II and classical El Niño triggered an asymmetrical equatorial circulation throughout the Indo-western Pacific (IWP) and thereby stimulated the Southern Annular Mode (SAM) through troposphere and stratospheric pathway mechanism. In addition, in 2015, SAM impacted the Indian Ocean, which intern affected ISM rainfall. Positive SAM associated with westward shift of anticyclone over south of Australia alters the circulation by inducing westerly winds over the South Indian Ocean, thereby suppressing Indian Ocean Dipole (IOD), and inducing drought conditions over India during 2015. Moreover, the AUS index, an indicator for IOD strength in boreal summer, is a bridging factor prevalent over mid-latitude regions in the southern hemisphere. Results from this study indicate the complex interaction of southern hemisphere atmospheric flow and its role in modulating the Indian Ocean region thereby ISM rainfall. A better understanding of these underlying mechanism can significantly enhance the predictive skills and projections of monsoon variability and extremes.