We used the samples from International Ocean Discovery Program (IODP) Hole U1505C in the northern South China Sea (SCS) to reconstruct the upper ocean profiles and discussed the East Asian Monsoon (EAM) variations during 15.0–12.5 Ma. 15 genera and 41 species were identified, and 7 planktonic foraminifer datums were recognized, then a reliable chronostratigraphic framework was updated. A principal component analysis (PCA) was used to identify the suitable assemblages for reconstructing upper water profiles, based on planktonic foraminifera relative abundance and isotope records. The sea surface temperature (SST), paleo-productivity, and the depth of thermocline (DOT) were reconstructed by the content of warm water species, high productivity species, and the ratio of mixed layer to thermocline species, respectively. Three main phases were identified: (1) during 15.0–14.7 Ma, the SST and paleo-productivity were high, while the thermocline was shallow, indicating a warm and rainy climate influenced by East Asian Summer Monsoon (EASM); (2) during 14.7–13.8 Ma, the SST was lower, the paleo-productivity increased significantly, and the thermocline deepened, indicating an enhanced East Asian Winter Monsoon (EAWM); (3) during 13.8–12.5 Ma, the SST increased slightly, the paleo-productivity deceased, while the DOT showed neglectable change, indicating a stable EAWM and a waning EASM. The results of the Morlet wavelet spectrum revealed that EAM and the upper ocean profiles in the northern SCS were predominantly regulated by the eccentricity cycles, emphasizing the significant impact of low-latitude processes on climate variations.