Earth's lower mantle is generally believed to be seismically and chemically homogeneous because most of the key seismic parameters can be explained using a simplified mineralogical model at expected pressure-temperature conditions. However, recent high-resolution tomographic images have revealed seismic and chemical stratification in the middle-to-lower parts of the lower mantle. Thus far, the mechanism for the compositional stratification and seismic inhomogeneity, especially their relationship with the speciation of iron in the lower mantle, remains poorly understood. We have built a complete and integrated thermodynamic model of iron and aluminum chemistry for lower mantle conditions and from this model has emerged a stratified picture of the valence, spin, and composition profile in the lower mantle. Within this picture the lower mantle has an upper region with Fe3+-enriched bridgmanite with high-spin ferropericlase and metallic Fe and a lower region with low-spin, iron-enriched ferropericlase coexisting with iron-depleted bridgmanite and almost no metallic Fe. The transition between the regions occurs at a depth of around 1600 km and is driven by the spin transition in ferropericlase, which significantly changes the iron partitioning and speciation to one that favors Fe2+ in ferropericlase and suppresses Fe3+ and metallic iron formation. These changes lead to lowered bulk sound velocity by 3–4% around the middle-lower mantle and enhanced density by ~1% toward the lowermost mantle. The predicted chemically and seismically stratified lower mantle differs dramatically from the traditional homogeneous model.