The Miocene Climate Optimum (MCO, ~17-14 Ma) provides an analogue for current global warming to investigate the interaction between climate change and carbon cycle. Yet, how deep-ocean carbon storage responds to climate change still remains poorly understood, mainly due to the scarcity of continuous, high-resolution carbon archives. Here, our high-resolution benthic B/Ca data reveals that carbonate ion concentration (CO₃^2-) changes synchronously with benthic oxygen (δ¹⁸O) and carbon isotopes (δ¹³C) on eccentricity timescales. By further box-model simulations, we hypothesize that eccentricity maxima tended to shrink the ice volume, resulting in a sea-level rise and a depletion of seawater δ¹⁸O. Meanwhile, massive carbonate accumulation over the flooding continental shelves facilitated consuming more alkalinity and sequestrating ¹³C in shallower water, which caused a decrease of sea water δ¹³C and CO₃^2- in deep sea. This study highlights the importance of the distribution of carbonate burial between continental margins and pelagic environments.