Variability of the East Asian winter monsoon (EAWM), stronger during glacials and weaker during interglacials, has been tightly linked to the wax and wane of the Northern Hemisphere ice sheets (NHIS) via the Siberian High over the last 2.8 million years (Myr). However, the long eccentricity cycle (ca. 400 kyr) in the EAWM record from the late Pliocene to early-Pleistocene (2.8–1.2 Ma) could not be linked to NHIS changes, which lacked the long eccentricity cycle in the Pleistocene. Here, we present the first low latitude EAWM record of the last 2.8 Myr using surface and subsurface temperature difference from the northern South China Sea to evaluate interactions between tropical ocean and EAWM changes. The results show that the EAWM variability displayed significant 400 kyr cycle between 2.8 Ma and 1.2 Ma, with weak (strong) EAWM during high (low) earth orbital eccentricity state. A super El Niño–Southern Oscillation (ENSO) proxy record, calculated using west-east equatorial Pacific sea surface temperature differences, revealed 400 kyr cycles throughout the last 2.8 Myr with warm phase during high eccentricity state. Thus, we propose that super ENSO mean state strongly modulated the EAWM strength through remote forcing to generate the 400 kyr cycle between 2.8 Ma and 1.2 Ma, while low NHIS volume was not sufficient to dominate the EAWM variation as it did over the last 0.9 Myr with 100 kyr cycles in dominance.