Significant contrast in sea surface salinity (SSS) emerges between the Arabian Sea (AS) and Bay of Bengal (BoB) caused by distinct air-sea freshwater flux and runoff inputs. The monsoon-induced inter-basin water exchange plays an important role in regional salinity balance and atmosphere-ocean feedback in the North Indian Ocean. The satellite SSS dataset reveals that significant intraseasonal variabilities of SSS occur in the south of India with stronger amplitude in winter than in summer. A case study in the late fall and earlier winter of 2016 shows that the Northeast Monsoon Current (NMC) and an eddy pair developed in the south of India plays a vital role in the intraseasonal variabilities of SSS there. In November, the East India Coasta Current (EICC) transports the low-salinity water southward to the east side of Sri Lanka. Meanwhile, a cyclonic eddy develops and propagates westward in the south of the NMC. Both NMC and the cyclonic eddy advects the low-salinity water westward to the south of India. Then, an anticyclonic eddy generates in the north of the NMC, forming an eddy pair with the cyclonic eddy. This eddy pair develops and propagates westward in the south of India for more than one and a half months, transporting low-salinity water westward. The perturbation of eddies and SSS gradient leads to the significant intraseasonal variability of SSS there.