Based on Argo observations and a coupled atmosphere–ocean–wave model, the upper ocean responses to the tropical cyclone (TC) Mekunu (2018) were investigated, and the role of a pre-existing cold eddy in modulating the temperature response to TC Mekunu was quantified by employing numerical experiments. With TC Mekunu’s passage, the mixed layer depth (MLD) on both sides of its track significantly deepened. Moreover, two cold patches (<26 °C) occurred, where the maximum cooling of the mixed layer temperature (MLT) reached 6.62 °C and 6.44 °C. Both the MLD and MLT changes exhibited a notable rightward bias. However, the changes in the mixed layer salinity (MLS) were more complex. At the early stage, the MLS on both sides of the track increased by approximately 0.5 psu. When TC Mekunu made landfall, the MLS change around the track was asymmetric. Significantly, a cold eddy pre-existed where the second cold patch emerged, and this eddy was intensified after TC Mekunu’s passage, with an average sea surface height reduction of approximately 2.7 cm. By employing the stand-alone ocean model, the numerical experimental results demonstrated that the pre-existing cold eddy enhanced TC-induced MLT cooling by an average of approximately 0.41 °C due to steeper temperature stratification at the base of mixed layer. Moreover, heat budget analysis indicated that the pre-existing cold eddy also enhanced subsurface temperature cooling mainly through zonal advection.