This study employed a regional earth system model, namely ROM over the CORDEX-SA domain, to investigate the future changes in the Marine heatwaves (MHWs) with respect to the historical baseline period (1976–2005) in the three time-slices, explicitly, near future (NRF; 2010–2039), middle future (MDF;2040–2069), and far future (FRF; 2070–2099) under two emission scenarios, Representative Concentration Pathway (RCP4.5 and RCP8.5). For the historical period, ROM showed a reasonable agreement with observed MHWs metrics and their trends and outperformed the forcing General Circulation Model and Multi-Model Ensemble of CMIP5 models. The future MHWs are expected to increase in intensity and duration. The continuous lengthening of MHWs duration leads to a permanent MHW state condition with strong spatial variability in its appearance. The first permanent MHW will emerge in both RCPs, while the absolute permanent MHW state is mainly visible in RCP8.5. The genesis and augmentation in the MHWs intensity is associated with local air-sea fluxes, however, in the long term, the increase in the mean SST in the future led to the rise of MHWs activity. The diagnosis of El Niño Southern Oscillation teleconnection and Indian Ocean Dipole on the MHWs is investigated. During the El Niño regime, not only did the proportion of the Tropical Indian Ocean experiencing MHWs increase but also an increase in the intensity is evident. IOD controls the MHWs metrics in the proximity of the western box and eastern box during its positive and negative phases.