We reinvestigated the Pleistocene calcareous nannofossil biostratigraphy of Site U1431D (International Ocean Discovery Program (IODP) Expedition 349) in the South China Sea (SCS). Twelve calcareous nannofossil Pleistocene datums are identified in the site. The analysis confirms that the last occurrence (LO) of Calcidiscus macintyrei is below the first occurrence (FO) of large Gephyrocapsa spp. (>5.5 μm). The FO of medium Gephyrocapsa spp. (4–5.5 μm) is also identified in the samples through morphometric measurements, which was unreported in shipboard results. Magnetobiochronologic calibrations of the numerical ages of LO of Pseudoemiliania lacunosa and FO of Emiliania huxleyi are underestimated and need reassessment. Other potential markers such as a morphological turnover of circular to elliptical variants of Pseudoemiliania lacunosa and a small Gephyrocapsa acme almost synchronous with the FO of Emiliania huxleyi may offer biostratigraphic significance in the SCS. The morphologic changes in Gephyrocapsa coccoliths are also examined for the first time in Site U1431D. Placolith length and bridge angle changes are comparable with other ocean basins, suggesting that morphologic changes are most likely evolutionary novelties rather than being caused by local climate anomalies.