Rapid changes on nutrient supply and CO2concentration that occurred in the northern South China Sea(SCS)during the Early Oligocene, provides an ideal natural laboratory, allowing us to peer into the coccolithophores’ physiology in the geological records. In this study, we established a new nannofossil assemblage index, termed as E* ratio, which is calculated by the relative abundance of eutrophic taxa and meso-oligotrophic taxa(E*=E/(E+C)×100, where e is eutrophic taxa, and c is meso-oligotrophic taxa). Eutrophic taxa include small Reticulofenestra, Reticulofenestra lockeri group, Reticulofenestra bisecta group and Coccolithus pelagicus group,while meso-oligotrophic taxa include Cyclicargolithus spp. The E* ratio is well correlated with nutrient proxy during the Early Oligocene, while with different covarying patterns under the higher and lower CO2condition. By comparing the assemblage changes to the published data, we suggest that coccolithophores may change the way they use carbon source and nutrient with the decline of CO2. Furthermore, this implies a possible initiation of the carbon concentrating mechanism.