There are phenocryst clinopyroxenes, phenocryst olivines and phenocryst amphiboles in Cenozoic basalts dredged from the South China Sea. Most of clinopyroxenes are resorbed into rounded shape and have narrow reaction rims. Phenocryst clinopyroxenes with characteristics of megacryst are crystallized from parent magma which have the same source with the host lavas. Without long time crystallization, clinopyroxenes are carried up to the surface so that they don't have shape of megacryst. Clinopyroxene has lower REE abundance, and its REE content shows a heavily depletion of HREE and LREE in comparison with MREE. The LILE (such as Rb, Ba, Sr) and HFSE (such as Nb, Zr) show heavily depletions in comparison with Hf which shows lightly enrichment. Nb/Ta and Zr/Hf show obvious fractionation features. Th shows lightly enriched but Pb heavily depleted. This study shows the source of clinopyroxene is relatively simple. As a result of mantle plumes, they are not affected by the interaction between mid ocean ridge and mantle plumes. Due to the fast rising of parent magma, the pressure drops rapidly and lots of olivines crystallize out from magma. All these factors result in the variation of magma composition and finally lead to the disequilibrium of both composition and texture between clinopyroxene and host lavas.