A long-term increase in coccolith size over the Pleistocene has long been discovered in global oceans. Such a long-term and evolutionary change is expected to exert substantial impact on the carbon cycle as coccolithophores are one of the major components of marine carbonate counter pump (CCP). Here, we present coccolith morphological data as well as coccolith calcite export at Ocean Drilling Program Site 1143 in the South China Sea over the past 2 Myr. The results confirm the idea that Earth eccentricity controlled coccolith size diversity and calcite export production in tropical oceans in the Pleistocene. In addition, we consider a possible origin of the long-term increase in coccolith size as a result of increased oceanic alkalinity availability. As coccolithophores evolved simultaneously in global oceans, the increased coccolith calcification may have promoted global marine particulate inorganic carbon production, especially for the interglacial stages. Therefore, the enhanced coccolith-based CCP may account for a stepwise increase in interglacial CO2 levels over the middle Pleistocene. High CO2 levels at the onset of the interglacial stages may reduce the glaciation rate, thereby prolonging an entire interglacial-glacial cycle after the middle Pleistocene. •Long-term increase in coccolith size can result from increased availability of oceanic alkalinity.•Long-term increase in coccolith size may promote global PIC production over the Pleistocene.•Increased coccolith calcification may account for a long-term interglacial CO2 change over the MPT.