The Middle Miocene East Antarctic ice sheet expansion (EAIE), which is indicated by an abrupt ~1‰ increase in global benthic foraminiferal δ18O at ~13.8 Ma, marks the Middle Miocene climate transition (MMCT) and has been related to astronomically modulated changes in the global carbon cycle. Here, we present high resolution (3–4 kyr) benthic foraminiferal δ18O and δ13C records from IODP Site U1337 in the central equatorial Pacific, which spans the period 12.2–15.8 Ma. The isotopic records clearly demonstrate significant imprints from periodic variations in the Earth's orbital parameters, particularly the obliquity (40 kyr) and the long eccentricity (400 kyr) cycles. While the benthic δ18O and δ13C exhibit nearly identical amplitudes for glacial-interglacial cycles from 15.8 to 12.2 Ma, the long-term trends in the benthic δ18O and δ13C had started to reverse after the beginning of the EAIE. Within the 400-kyr band, the benthic −δ18O and δ13C displays a constant phase relationship between 15.8 and 12.2 Ma. At the 41-kyr band, however, a phase reversal reaching >180° between −δ18O and δ13C occurs from 13.8 Ma to 14.0 Ma during the period of the EAIE. A similar phase relationship of benthic foraminiferal −δ18O and δ13C at the 400-kyr band and the 41-kyr band is also observed at ODP Site 1146 from the northern South China Sea. This phase jump occurs when the long-term trends in δ18O and δ13C split, suggesting a decoupling of the global ice volume and ocean carbon reservoir changes during the Middle Miocene.