A general feature of the late Miocene ocean carbon cycle changes can be characterized by secular 405-kyr long-eccentricity cycles in ocean dissolved inorganic carbon isotopic composition (δ 13C), superimposed by a permanent negative δ 13C excursion, namely, the Late Miocene Carbon Isotope Shift (LMCIS). The late Miocene epoch is a critical period during which the Earth experienced long-term cooling, reflecting a climatic transition from coolhouse to icehouse. Whereas, the globally composited deep ocean oxygen composition (δ 18O) do not show a straightforward increase which would indicate cooling of deep water and/or increased land ice sheet volume. Atmospheric CO2 reconstructions do not show a parallel change with the LMCIS or the late Miocene cooling based on our present knowledge. These incompatible climatic records could originate in the interactions between Earth’s carbon cycle and climate system, which remains unclear during the late Miocene period. This study presents new benthic foraminiferal isotopes from International Ocean Discovery Program Site U1560 in the South Atlantic. Together with previously published late Miocene benthic δ 13 C records, we reexamine the patterns of benthic δ 13 C in global oceans. Our analysis indicates a long-term increase in the benthic δ 13C gradient between the Atlantic and Pacific oceans over the late Miocene. The intensified basinal δ 13 C gradient agrees with a long-term and step-wise increase in the benthic δ 18O at Site U1560 in the South Atlantic. A diagnostic carbon cycle box-model developed in this study and several lines of geological evidence support a sluggish or weakening of ocean overturning circulation due to enhanced Antarctic glaciation as a driver for the intensified basinal δ 13 C gradient over the late Miocene.