The dataset compiles morphological measurements of coccoliths (Gephyrocapsa spp. and Emiliania huxleyi, >2µm) from surface samples of the South China Sea retrieved along a depth gradient (629 – 3809 m) during the R/V Sonne cruises (SO-95). The morphological attributes (length, volume, thickness, and ks shape factor) from the Noelaerhabdaceae group (Emiliania huxleyi and Gephyrocapsa spp) were applied to evaluate coccolithophore calcification and preservation aspects. The length, volume, area, and mass were obtained using the C-Calcita software from images taken under a cross-polarized microscope (Zeiss AX10). Thickness and the shape factor ks were calculated. The columns include station names, Longitude, Latitude, Depth (m), number of coccoliths measured per sample, mean ks shape factor, thickness, length, volume, mass, and standard deviation of mean ks/mean ks.