The Intermediate Waters formed in the Southern Ocean are critical for ventilating the thermocline in the Southern Hemisphere Gyres and transporting climatic signals from high to low latitudes on glacial- interglacial time-scales. Despite the importance of the Southern Ocean Intermediate Waters (SOIWs), information on past changes in SOIWs formation is fragmentary, and its impact on the South Pacific Gyre (SPG)’s thermocline largely unknown. Here, we present a 200 kyr record of paired Mg/Ca ratios and stable oxygen isotope from surface and deep dwelling planktonic foraminifera, from the SPG. On average, the Globigerina bulloides Mg/Ca-derived sea surface temperatures show similar conditions during the LGM and Marine Isotope Stage (MIS) 6 (9.4 ◦ C versus 9.8 ◦ C). In contrast, the subsurface temperatures derived from the Mg/Ca values of Globorotalia inflata and Globorotalia truncatulinoides suggest that LGM is ∼3 to ∼2 ◦C colder than MIS 6. Furthermore, at subsurface depths the reconstructed δ18Osw-ivc record (proxy for relative local salinity changes) suggests opposite glacial conditions, with slightly saltier- than-Holocene waters during MIS 6, and fresher-than-Holocene waters during LGM. Contrasting glacial scenarios, plausibly due to changes in the presence of SOIWs at the study site, suggest variable formation and/or advection of SOIWs to the SPG during different glacial stages. The variability in SOIWs is probably driven by the changes in the intensity of the Southern Westerly Winds.