The late Permian Emeishan large igneous province (ELIP) in SW China is a melting product of the Emeishan mantle plume. Recently, it has been debated whether peridotite or pyroxenite is the dominant lithology of the mantle source in the ELIP. To address this, systematic analyses of bulk-rock and coexisting spinel and olivine compositions were conducted on picrites from Lijiang–Yongsheng, Dali–Binchuan, Yumen, Muli, and Ertan. The ELIP picrites exhibit positive TiO2–CaO and negative MgO–CaO correlations, as well as low FC3MS values (−0.24–0.1), supporting a peridotite-dominated mantle source. This lithology of the mantle source is also supported by the high 100 × Mn–Fe (1.43–1.73) and Mn–Zn (13.6–18.4) values but low 10,000 × Zn–Fe (8.0–12.7) ratios of the olivine phenocrysts. The estimated mantle potential temperature for Lijiang, Yongsheng, Yumen–Ertan, Muli, and Dali–Binchuan picrites decreased away from Lijiang and Yongsheng, suggesting that the Lijiang and Yongsheng areas were the center of the ELIP. The Lijiang–Yongsheng primary magma shows similar SiO2 content but lower Al2O3 contents (average of 8.24 wt.%) and higher MgO contents (average of 21.42 wt.%) than those of Dali–Binchuan primary magma (Al2O3: 9.86 wt.%; MgO: 19.02 wt.%). Also considering the high Gd–Yb (average of 3.05) and La–Yb (average of 14.61) ratios and mantle potential temperature (average of 1599 °C), we proposed that Lijiang–Yongsheng lavas are produced via the melting of a garnet–peridotitic mantle. In contrast, the Dali–Binchuan lavas with low Gd–Yb (average of 1.91) and La–Yb (average of 5.88) ratios can be explained by their formation in the garnet–spinel transition zone of a peridotitic mantle. The Yumen–Ertan primary magma displays similar mantle potential temperature (average of 1600 °C), Al2O3 and FeO content, and Gd–Yb ratios to those of Lijiang–Yongsheng lavas, indicating that YumenvErtan primary magma may be attributed to the partial melting of garnet with minor peridotite. Therefore, heterogeneous plume-head mantle sources lead to the evaluation of melting conditions of the late Permian ELIP picrites.