Using the numerical calculations of exposure time ((Formula presented.)), this study investigated the three-dimensional characteristics of water exchanges associated with the coastal-shelf circulations of the Northern South China Sea (NSCS). The circulation connectivity and its interannual variability under the modulation of El Niño Southern Oscillation (ENSO) were investigated. The (Formula presented.) gradually increased from approximately 50 days over the outer shelf to more than 150 days in the shallower coastal seas with the Beibu Gulf displaying a significantly longer (Formula presented.) (approximately 300 days). The Beibu Gulf played an influential role in the water exchange that had a contribution of over 30% to (Formula presented.) in the most regions. The results from sensitivity experiments indicate that the wind forcing is the primary controller of (Formula presented.) and the boundary flux plays a secondary role. Specifically, the wind enhances water exchange in western NSCS, particularly in the Beibu Gulf and Yuexi region. Conversely, boundary fluxes facilitate exchanges in the eastern shelf, such as Yuedong region. Analysis revealed a clear modulation from ENSO on water exchange, wherein El Niño and La Niña years displayed symmetrical morphologies in (Formula presented.) distribution anomalies, albeit with varying intensities. During El Niño years, the weakened southwestward shelf current increased (Formula presented.) and the shelf water was less likely to reach the Beibu Gulf, and once arrived, these waters were trapped inside to elongate (Formula presented.). In contrast, during La Niña years, the strengthened southwestward shelf current shortened (Formula presented.) and more shelf waters were transported away from the NSCS by an intensified southwestward shelf current.