Large igneous provinces (LIPs) are often associated with mass extinctions and are thus vital for life evolution on Earth. However, the precise relation between LIPs and their impacts on biodiversity is enigmatic as they can be asynchronous. If the environmental impacts are primarily related to sill emplacement, the structure of LIPs’ magma storage system becomes critical as it dictates the occurrence and timing of mass extinction. Here we use surface wave tomography to image the lithosphere under the Permian Emeishan Large Igneous Province (ELIP) in southwestern China. We find a NE-trending zone of high shear-wave velocity (Vs) and negative radial anisotropy (Vsv > Vsh) in the crust and lithosphere and interpret it as a mafic-ultramafic, dike-dominated magma storage system on the hidden hotspot track of the ELIP. An area of less-negative radial anisotropy, on the hotspot track but away from the eruption center, reflects an elevated proportion of sills emplaced at the incipient stage of the ELIP. Liberation of poisonous gases and mercury by the sills explains why the mid-Capitanian global biota crisis preceded the peak ELIP eruption by 2-3 million years.