Based on core-top calibration, the TEX86H-derived temperature has been considered as representing subsurface sea temperature (SSST), and the difference between the U37K′-derived sea-surface temperature (SST) and the TEX86H-derived SSST can be used to reflect the depth of thermocline (DOT) in the South China Sea region (Jia et al., 2012). We evaluated the DOT dynamics in late Quaternary records using this approach on paired analysis of samples from core MD05-2896/7 in the southern South China Sea. The reconstructed DOT over the last 180,000 yr (180 ka) displays a shoaling trend in glacial periods, which may be attributed to the strengthened cyclonic gyre by the enhanced East Asian winter monsoon and Walker circulation with prominent La Niña-like state, and vice versa in interglacial periods corresponding to reduced winter monsoon with enhanced El Niño-like state. These upper-water thermal variations testify that enhanced winter monsoon was the direct cause of an uplifted local thermocline during glacial or La Niña-like states with strengthened cyclonic gyre due to positive wind stress curl in the southern South China Sea. Our results provide insights into the relationship between monsoon and ENSO on both glacial and millennial time scales.