The carbonate content, coccolith abundance, coccolith's contribution to carbonate, stable isotope ratios of bulk carbonate were analyzed in the late Pleistocene section of the site IODP U1433 in the South China Sea. This dataset is employed to study the carbonate source and coccoliths' contribution to bulk carbonate in the sediment blow carbonate compensation depth (CCD). The core was retrieved during the International Ocean Drilling Project 349, 2014, in the South China Sea. The bulk carbonate content was measured by Controlab NFP18–508 carbonate analyzer. The carbon and oxygen isotopic ratios of carbonate were analyzed by Finnigan MAT 252 mass spectrometer. The slides for coccolith abundance and morphological analyses were perpared following the “drop technique”. The light for thickness measurement were calibrated with a calcite wedge. The cococlith assemblages were analyzed following the taxonomy in Nannotax3 (https://www.mikrotax.org/Nannotax3/index.html). The coccolith contribution to carbonate was estimated with number of cococlith*mean coccolith mass/carbonate content.