The quantitative and objective characterization of dissolution intensity in fossil planktonic foraminiferal shells could be used to reconstruct past changes in bottom water carbonate ion concentration. Among proxies measuring the degree of dissolution of planktonic foraminiferal shells, X-ray micro-Computed Tomography (CT) based characterization of apparent shell density appears to have good potential to facilitate quantitative reconstruction of carbonate chemistry. To assess the accuracy and reliability of the proxy based on X-ray micro-CT scanning, we evaluated the planktonic foraminiferal shell dissolution intensity using seafloor sediment samples obtained at 13 sites in the South Atlantic Ocean. The sea floor sediment samples are located at water depth ranging between 940 and 4401 m. The data of benthic foraminiferal shell B/Ca ratio in these sediment samples have been measured by previous studies. The CT-based Dissolution Index (CTDX) of four species of planktonic foraminifera (G. bulloides, G. inflata, G. ruber, and T. sacculifer) at each site are provided. We also offered each individual's CT number histogram data, which was used for calculating CTDX.