Magnesite (MgCO3) entering the lower mantle together with the subducted oceanic crust is an important carbon carrier. The reaction between magnesite and mantle minerals has been documented, but its influence on the density and velocity profiles of lower mantle remains unexplored. To decipher the deep carbon transportation and its associated effect, here we determined the thermal equations of state of magnesite up to 120 GPa and 2600 K using X‐ray diffraction in laser‐heated diamond anvil cells. The obtained thermal elastic parameters of magnesite facilitated a comprehensive understanding on the influence of magnesite‐SiO2 reaction, variation of carbon and SiO2 content, and temperature on the origin of lower‐mantle scatterers at 1,000–1,800 km depth. Our modeling revealed that the depth of the lower‐mantle VS scatterers is mainly controlled by the Al2O3 content in SiO2, while its magnitude depends on the SiO2 content. Along normal geotherm, the magnesite‐SiO2 reaction would occur before the post‐stishovite transition, consuming substantial SiO2 in the subducted oceanic crust. Depending on the amount of residual SiO2, the post‐stishovite transition can produce a 2.5–5.2 (2)% VS reduction, compatible with the observed seismic scatterers in Izu‐Bonin and Mariana subduction zones. Along slab geotherm, this reaction occurs after the post‐stishovite transition, generating a greater VS reduction of 4.4–6.4 (4)%. We thus propose that the reaction between sinking MgCO3 and SiO2 in the slab is one of the potential factors influencing the magnitude of the lower‐Vs scatterers at 1,000–1,900 km depth. Our results provide new insights into the deep‐mantle carbonate transportation influencing regional geophysics.