<p>Human activities have caused marked global warming, which has in turn substantially intensified the global water cycle and affected oceanic physics. However, a widely accepted understanding of how the climate system responds to freshwater flux (FWF) forcing under future warming scenarios remains elusive. In this study, we examine salinity changes driven by FWF forcing and their impact on El Niño-Southern Oscillation (ENSO), using experiments from the Flux-Anomaly-Forced Model Intercomparison Project (FAFMIP) with the Flexible Global Ocean–Atmosphere–Land System model, grid-point version 3. Our results show that variability in sea surface salinity (SSS) in the tropical Pacific increases by 5.9% due to FWF forcing, which freshens the upper ocean in the western Pacific warm pool. This leads to a decrease in salinity across the tropical Pacific, enhancing the east–west contrast in SSS. These salinity changes result in a shallower mixed layer, which strengthens upper-ocean stratification and stability. Furthermore, changes in salinity variability modulate sea surface density, affecting the mixing and entrainment processes at the bottom of the mixed layer during ENSO, ultimately trapping more heat in the surface ocean. Our findings suggest that FWF forcing reduces ENSO intensity by 12% during La Niña events and increases it by 22% during El Niño events, enhancing ENSO asymmetry by 28%. Under future global warming, El Niño events are expected to intensify, while La Niña events are likely to weaken. The FAFMIP experiments provide valuable insights into ways how ocean salinity distribution responds to FWF forcing under global warming, improving our understanding of ENSO diversity.</p>