An interdecadal shift in the onset date of the South China Sea summer monsoon (SCSSM) is identified during the late 1990s by using the European Centre for Medium-Range Weather Forecasts Interim Reanalysis dataset. The mean onset date was brought forward by two pentads during 1999–2013 compared to that during 1979–1998. The large-scale atmospheric and oceanic change associated with this shift exhibits a significant interdecadal variation signal around 1998/1999, indicating that the shift during the late 1990s is robust. Different from the well-known mid-1990s shift, this shift carried more important systematical significance. Diagnostic analysis suggests that the earlier outbreak of the SCSSM was due to the interdecadal warming of the warm pool, which brought stronger convection anomalies and led to a weak western Pacific subtropical high (WPSH) during boreal spring (March–May). The earlier retreat of the WPSH was a direct cause of this shift.