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The southeastern Indian Ocean (SEIO) exhibits prominent decadal variability in sea surface salinity (SSS), showing salinity decreases during 1995-2000 and 2005-2011 and increases during 2000-2005 and after 2011. These salinity changes are linked to the Indo-Pacific climate and have impacts on the regional marine environment. Yet, the underlying mechanism has not been firmly established. In this study, decadal SSS variability of the SEIO is successfully simulated by a high-resolution regional ocean model, and the mechanism is explored through a series of sensitivity experiments. The results suggest that freshwater transport of the Indonesian throughflow (ITF) and local precipitation are two major drivers for the SSS decadal variability. They mutually cause most of the variability, with a generally larger contribution of precipitation. Other processes, such as evaporation and advection driven by local winds, play a minor role. Further analysis shows that the decadal precipitation in the SEIO is mainly associated with the decadal variability of Ningaloo Niño. Ocean dynamic processes significantly modify the relationship between SSS and precipitation, greatly shortening their lag time. The changes in both volume transport and salinity of the ITF water can cause large salinity changes in the SEIO region. Although local wind forcing gives rise to considerable changes in evaporation rate and ocean current advection, its overall contribution to decadal SSS variability is small compared to local precipitation and the ITF.