The passage of typhoons usually induces a pronounced upper ocean response that is not only determined by typhoon attributes but also modulated by pre-existing mesoscale eddies. Here we examined the upper ocean response to Typhoon Nakri (2019) in the South China Sea, which first passed over a cold eddy following a straight path and then made a sudden turning over a warm eddy, on the basis of satellite observations and HYbrid Coordinate Ocean Model (HYCOM) reanalysis datasets in addition with numerical experiments. Two cold and salty patches with remarkable sea surface temperature (SST) cooling and sea surface salinity (SSS) increase emerged after Typhoon Nakri's passage in the pre-existing cold-eddy and warm-eddy regions. Particularly, the maximum SST cooling and SSS increase induced by Typhoon Nakri reached 6.6 °C and 1.6 psμ in the pre-existing warm-eddy region, which were even more pronounced than those in the pre-existing cold-eddy region (6.0 °C and 1.3 psμ). Typhoon Nakri enlarged the cold eddy and weakened the warm eddy significantly, with the maximum sea surface height reduction (up to 43 cm) appearing in the pre-existing warm eddy, which even disappeared after Nakri. Furthermore, Nakri induced phytoplankton blooms with a chlorophyll-a concentration increase reaching 2 mg m−3. The subsurface temperature (salinity) was also reduced (increased) significantly in the pre-existing warm-eddy region. The more pronounced ocean response in the warm-eddy region was largely attributed to the sudden turning of Nakri's track, prolonging the forcing time of typhoon winds. By employing the three-dimensional Price–Weller–Pinkel model, the results of numerical experiments demonstrated that typhoon's track turning as well as the accompanied slow translation speed during Nakri's sudden-turning stage, played a predominate role in resulting in the remarkable SST cooling within the warm-eddy region. These results highlight the important role of sudden track turning in modulating the upper ocean response to typhoons.