Upwelling off Vietnam in the South China Sea (SCS) and the Sumatra–Java upwelling in the Indian Ocean significantly modulate regional variation in climate. Although located in different hemispheres, these upwellings nearly concur during the boreal summer; both are the result of wind-induced Ekman divergence. Beyond seasonal time scales, the two upwellings were not synchronous in 1998. In the summer of 1998, upwelling off Vietnam was almost absent, generating the warmest summer on record in the SCS. We demonstrated that the El Niño–Southern Oscillation, which was highly correlated with the upwelling in previous studies, was not solely responsible for this variability. Wind trajectory analyses revealed that cross-equatorial winds, which had passed over the Sumatra–Java upwelling site about 2 weeks earlier, were a rapid force acting on SCS summer upwelling. In the summer of 1998, SCS winds were greatly perturbed due to an anomalous wind path that blew toward the SCS through the Sulu Sea. Our findings suggest that not only the resulting weakening but also the perturbation of the SCS winds prevented the formation of summer upwelling off central Vietnam in that year.