The coccolithophore widely distributed in marine environment is one of the most important algae. Coccolith, formed through biomineralization processes, has important significance in paleoceanographic study. Interactions between marine clay minerals and organic matters play an important role in the global carbon cycle. Representative coccolithophore Emiliania huxleyi and marine clay minerals of illite and montmorillonite were selected for experimental co-culturing study. Growth curves, elemental ratios of Sr/Ca and Mg/Ca, UV-Vis spectra, FTIR spectra and XRD were utilized for analysis. The results show that illite has an insignificant effect on E. huxleyi, whereas montmorillonite has significant influence on E. huxleyi in growth curves as well as element ratios of Mg/Ca and Sr/Ca due to its adsorption and flocculation effect on nutrients. Metabolic biomolecules fail to enter the interlayer of illite. However, biomolecules secreted by the E. huxleyi enter and are stored in the interlayers of montmorillonite. The presented study indicates that the interaction between marine clay mineral of montmorillonite and marine microorganisms has important geological significance, and hence geo-biologists should pay more attention to the study of the ancient marine environment.