As the most prominent interannual climate variation on Earth, El Niño - Southern Oscillation (ENSO) alters the pattern of salinity variability worldwide by both atmospheric and oceanic dynamics and processes. Investigating salinity provides a useful perspective for understanding the ENSO evolution and prediction. Previous studies have mainly focused on the salinity at sea surface (SSS) or mixed layer, the salinity changes at subsurface and the basin-wise salinity changes are less explored. This study provides an observational based analyses on the global and regional salinity changes related to ENSO from surface to 2000m, and explores the drivers by exploring the surface freshwater flux changes. Results confirm a strong negative sea surface salinity anomaly (SSS) in the tropical central and western Pacific Ocean during EI Niño, caused by anomalously eastward currents and negative freshwater flux anomaly. The salinity change at the near-surface layer (0-100m) is opposite to subsurface (100-300m) for the global average, probably associated with the tropical thermocline changes. Sea surface salinity (SSS) in the tropical oceans decreases during El Niño, and the tropical Atlantic Oceans shows an increase of salinity during El Niño, partly offsetting the tropical Pacific and Indian freshening for the tropical oceans as a whole.