The Late Permian Emeishan flood basalts, with thickness over 5000 meters at Binchuan area in western margin of the Yangtze craton, consisted mainly of tholeiitic basalts and minor alkaline basalts. Based on petrography, major and trace element data, the tholeiitic basalts could be classified into two major geochemical types: low-Ti (LT) and high-Ti (HT) basalts. The LT type lavas, occurred in the lower-middle part of petrologic column, exhibited lower Ti/Y (<500), ∑REE (<120), (La/Yb)N (<6), (Sm/Yb)N (<2.0) and higher Mg# (0.48～0.67); whereas the HT type lavas on the top of the petrologic column had higher Ti/Y (>500), ∑REE (>150), (La/Yb)N (>9), (Sm/Yb)N (>3) and lower Mg# (0.39～0.53). The LT could be further divided into two subtypes: LT1 and LT2. They occurred in the lower and middle parts of the petrologic column respectively. LT1 lavas exhibited relatively higher Mg# (0.61～0.67) and lower Nb/U ratio than that of the LT2 type lavas, and had positive Th and U anomaly. The LT and HT lavas might be originated from different mantle source under various melting conditions and underwent distinct differentiation and contamination processes. The LT lavas, with significant "crustal-source" signatures, might associate with the mobilization of enrichment component in lithosphere mantle. "Crustal source" signatures were getting less from the bottom (LT1) to the top (HT) of the petrologic column. LT lavas that might be formed at the main activity stage of the Emeishan plume, might be generated from the head of mantle plume with higher degree partial melting and then experienced weak garnet+clinopyroxene fractional crystallization. Late-waning stage formed HT lavas experienced lower degree of partial melting, and then underwent strong plagioclase dominated fractional crystallization process in the upper crust and little crustal contamination.