The Indo-Pacific Maritime Continent (MC) is the site of intense atmospheric convection, associated with the Walker Circulation, which significantly influences global climate. Observations reveal decreasing sea surface salinity (SSS) in the MC region since 1960, a consequence of enhanced freshwater flux. During this period observed sea surface temperature (SST) trends in the tropical Pacific exhibit La Niña-like patterns, the enhanced western tropical Pacific warming and eastern cooling, which is at odds with many climate model results. This study explores how MC freshening influences the La Niña-like pattern under global warming. Sensitivity experiments demonstrate that imposed MC freshening enhances near-surface stratification, shoaling the mixed layer and amplifying surface warming in the western Pacific. The intensified zonal SST gradient strengthens the Walker circulation, enhancing easterly winds, equatorial upwelling, and Equatorial Undercurrent (EUC) transport, thereby cooling the eastern Pacific. CMIP6 simulations analysis corroborates that salinity-modulated stratification critically shapes Pacific SST patterns, underscoring the need for improved observations and model representations of the MC region hydrological cycle associated upper ocean spatial and temporal thermohaline stratification patterns.