The middle Miocene (~16-13 Ma) is critical to understand the stepwise long-term cooling during Cenozoic, but the interactions between global ice volume and carbon cycle remains elusive for this major climate transition. In contrast to their anti-phased relationship during the late Quaternary, benthic foraminiferal 18O and 13C were highly coherent and in phase at the 100-kyr eccentricity band during the middle Miocene. Using a simple biogeochemical box model, we show that this coherent variation can be explained by sea-level-driven shelf-to-basin carbonate deposition shift which increased 13C at low eccentricity during cold glacial periods (i.e., high d18O), combined with a strengthened biological pump stimulated by enhanced riverine nutrient supplies which decreased 13C at high eccentricity during warm inter glacial periods (i.e., high 18O). This suggests that both high- and low-latitude processes - namely Antarctic ice sheet and monsoon changes, respectively - played critical roles in the middle Miocene carbon cycle on the eccentricity band. We further show that these processes can successfully explain the ~100-200 ppm atmospheric CO2 decline from 14.7 Ma to 14.5 Ma, with important implications for a major cooling transition during the late Cenozoic ice age.