Ore-bearing mafic–ultramafic layered intrusions are widespread in the Emeishan large igneous province (ELIP). The ore genesis and sulfide evolution/saturation in these layered intrusions remain debated, due to the lack of constraints on their parental magma compositions. Although trace element partition coefficients may be able to provide a reasonable estimate for the parental magma compositions, finding suitable partition coefficient for the parental magma composition calculation can be a challenge. This is due to the variability of potential mineral constituents, magma compositions, and crystallization temperature and pressure. In this study, we use the phenocryst-groundmass method and LA-ICP-MS analysis to establish new trace element partition coefficients and mathematical expression for the clinopyroxene (Cpx) in the ELIP basalts. Similarity in the estimated magma compositions (with our partition coefficients) to those of the Emeishan high-Ti basalts and the microgabbro chilled margin indicates that this method can reliably yield parental magma compositions for mafic plutons in the ELIP.