We present new deep water carbonate ion concentration ([CO_3^(2−)]) records, reconstructed using Cibicidoides wuellerstorfi B/Ca, for one core from Caribbean Basin (water depth = 3623 m, sill depth = 1.8 km) and three cores located at 2.3–4.3 km water depth from the equatorial Pacific Ocean during the Last Glacial–interglacial cycle. The pattern of deep water [CO_3^(2−)] in the Caribbean Basin roughly mirrors that of atmospheric CO_2, reflecting a dominant influence from preformed [CO_3^(2−)] in the North Atlantic Ocean. Compared to the amplitude of ∼65 μmol/kg in the deep Caribbean Basin, deep water [CO_3^(2−)] in the equatorial Pacific Ocean has varied by no more than ∼15 μmol/kg due to effective buffering of CaCO_3 on deep-sea pH in the Pacific Ocean. Our results suggest little change in the global mean deep ocean [CO_3^(2−)] between the Last Glacial Maximum (LGM) and the Late Holocene. The three records from the Pacific Ocean show long-term increases in [CO_3^(2−)] by ∼7 μmol/kg from Marine Isotope Stage (MIS) 5c to mid MIS 3, consistent with the response of the deep ocean carbonate system to a decline in neritic carbonate production associated with ∼60 m drop in sea-level (the “coral-reef” hypothesis). Superimposed upon the long-term trend, deep water [CO_3^(2−)] in the Pacific Ocean displays transient changes, which decouple with δ^(13)C in the same cores, at the start and end of MIS 4. These changes in [CO_3^(2−)] and δ^(13)C are consistent with what would be expected from vertical nutrient fractionation and carbonate compensation. The observed ∼4 μmol/kg [CO_3^(2−)] decline in the two Pacific cores at >3.4 km water depth from MIS 3 to the LGM indicate further strengthening of deep ocean stratification, which contributed to the final step of atmospheric CO_2 drawdown during the last glaciation. The striking similarity between deep water [CO_3^(2−)] and ^(230)Th-normalized CaCO_3 flux at two adjacent sites from the central equatorial Pacific Ocean provides convincing evidence that deep-sea carbonate dissolution dominantly controlled CaCO_3 preservation at these sites in the past. Our results offer new and quantitative constraints from deep ocean carbonate chemistry to understand roles of various mechanisms in atmospheric CO_2 changes over the Last Glacial–interglacial cycle.