Ocean heat content (OHC) plays an important role in controlling changes in Earth’s climate. However, relatively little research has been conducted into changes in OHC over a millennial scale, or into the mechanisms that control OHC migration in the ocean’s interior. This paucity of research is largely due to the lack of subsurface proxy records. Here, we analyzed planktonic Mg/Ca and δ18O records from species with different calcification depths to reconstruct the thermal structure of the water column and upper OHC changes since 21 kyr B.P. in the South China Sea. The results revealed that temperatures at intermediate and lower thermocline depths were warm during the last the deglaciation and became cool during the Holocene. The water cooling at ∼700 m began at 14.3 kyr B.P., but was delayed until 12.9 kyr B.P. at ∼325 m, and until 9.2 kyr B.P. at ∼250 m. In addition, upper thermocline temperatures at ∼100 m also started to decline at ca. 7.3 kyr B.P. Simultaneously, intermediate and thermocline OHC values were high during the last deglaciation, but surface OHC was low. We infer, therefore, that more heat was stored at intermediate depths during the last deglaciation, and that the upward release of the intermediate OHC resulted in the sequential delays in the cooling of intermediate to upper thermocline water. By combining these results with tropical Pacific records, we also hypothesize that the release of deeper OHC was perhaps the heat source for low-latitude processes during the Holocene.