Coccolithophores play a key role in the marine carbon cycle and ecosystem. The carbonate shells produced by coccolithophore, named as coccolith, could be well preserved in the marine sediment for millions of years and become an excellent archive for paleoclimate studies. The micro-filtering and sinking-decanting methods have been successfully designed for coccolith separation and promoted the development of geochemistry studies on coccolith, such as the stable isotopes and Sr / Ca ratio. However, these two methods are still not efficient enough for the sample-consuming methods. In this study, the trajectory of coccolith movement during a centrifugation process was calculated in theory and carefully tested by separations in practice. We offer a MATLAB code to estimate the appropriate parameter, angular velocity at a fixed centrifugation duration, for separating certain coccolith size fractions from bulk sediment. This work could improve the efficiency of coccolith separation, especially for the finest size fraction, and make it possible to carry out the clumped isotope and radio carbon analyses on coccoliths in sediment.