Interannual salinity variations in the Tsushima Strait are investigated on the basis of historical hydrographic data. The EOF analysis revealed that the most dominant mode is the in-phase salinity variation between the eastern and western channels. The time coefficients of the EOF first mode in summer show a negative correlation with the Changjiang discharge, which indicates that salinity in the Tsushima Strait tends to decrease over summer, related to a large discharge of the Changjiang. The eigenvectors of the first mode are larger in the eastern channel than those in the western channel, though the low salinity water mainly flows through the western channel. This is because the low salinity water spreads into the eastern channel as well as the western channel over summers with a large discharge of the Changjiang. The out-of-phase salinity variation between the channels is extracted as the EOF second mode; this is the predominant variation in the western channel. The time coefficients of the second mode in summer show no significant correlations to the volume transports through the western channel and the transport differences between channels. A relationship between the EOF second mode and variations in the wind stress over the East China Sea is suggested.