Quantifying changes in seawater carbonate chemistry is crucial to deciphering of patterns and drivers of the oceanic carbon cycle and climate change. Here, we present a new deep-water carbonate ion saturation state (Δ[CO32−]) record for the Pliocene western tropical Pacific, reconstructed from the size-normalized weight of the planktonic foraminifer Trilobatus sacculifer of IODP Site U1490. A steep decline in deep-water Δ[CO32−] occurred at ∼4.6 Ma synchronous to the enhanced production of North Atlantic Deep Water (NADW) related to the closure of the Panamanian Gateway. Subsequently, at the onset of the Northern Hemisphere glaciation at ∼2.7 Ma the weakening of NADW formation resulted in a deep-water Δ[CO32−] peak. The changes in NADW production rate likely controlled a seesaw-like fluctuation in deep-water Δ[CO32−] between the Pacific and Atlantic oceans. During the late Pliocene (∼3.8–2.8 Ma), Antarctic ice-sheet/sea-ice expansions sequestered CO2 in the deep Pacific through ventilation of the deep watermass, leading to a long-term decrease in deep Pacific Δ[CO32−]. We infer that fluctuating NADW production rates at ∼4.6 Ma and ∼2.7 Ma influenced inter-basinal fractionation of deep-ocean carbon between the Atlantic and Pacific, and that deep Pacific carbon storage linked to expansions of Antarctic ice sheet/sea ice contributed to the lowering of atmospheric pCO2 and global cooling during the late Pliocene.