Continental flood basalts typically exhibit large variations in their chemical and isotopic compositions, which are significantly different from those of oceanic basalts. However, the origin of these geochemical heterogeneities remains unclear. Here, new Hf-Mg-Sr-Nd isotope and trace element data for the picritic lavas from the Emeishan large igneous province are used to constrain primary magma compositions and nature of mantle sources of the continental flood basalts. Our results demonstrate that the high-Ti picrites from Maoniuping, Tanglanghe and Wuguijing exhibit high Hf/Hf* (0.9–1.1), Ti/Ti* (1.0–1.4) and coupled NdHf isotopes. In contrast, the low-Ti picrites from Daying exhibit significantly low Hf/Hf* (0.4–0.8), Ti/Ti* (0.4–0.8) and decoupled NdHf isotopes (higher ε_Hf relative to ε_Nd in the NdHf isotopic space relative to the mantle array). Most of the Emeishan picrites show normal-mantle like δ²⁶Mg values (−0.18 to −0.28‰). The high- and low-Ti picritic melts can be explained by partial melting of a hybrid mantle source containing subducted oceanic crust (in form of silica-poor pyroxenite) at relatively high pressures (3.0–5.0 GPa) and low pressures (2–3 GPa), respectively. Furthermore, marine sedimentary components characterized by extremely low Hf/Hf* (0.1–0.8), Ti/Ti* (0.02–0.59) and decoupled NdHf isotopes may have played an important role in the generation of the low-Ti picrites from Daying. Considering that the lithospheric mantle beneath this region has been modified by melts/fluids associated with the Neoproterozoic slab subduction, we speculate that these oceanic crustal materials are primarily derived from the Neoproterozoic subduction-modified lithospheric mantle. Interaction between mantle plume and subduction-modified lithospheric mantle may account for the chemical and isotopic heterogeneity in the picritic lavas associated with the Emeishan continental flood basalts.