The present-day Earth’s mantle is predominated by a spherical harmonic degree-2 structure with African and Pacific superplumes surrounded by subducted lithosphere, as revealed in seismic tomography studies. It has been demonstrated that such mantle structure is closely related to plate motion history for the last 120 million years (Ma). An important question is how the mantle structure has evolved from the distant past to the present-day. In this study, we first present three-dimensional spherical models of mantle convection with plate motion history since the Early Paleozoic for the last 500 Ma that includes the assembly and break-up of supercontinent Pangea. We then reconstruct temporal evolution of the surface and CMB heat fluxes and continental vertical motions since the Paleozoic. Our models reproduce well present-day observations of the surface heat flux, seafloor age distribution, bathymetry, and dynamic topography. As a consequence of the assembly and breakup of Pangea, the equatorial CMB heat flux reaches a minimum at ~270 Ma and again at ~100 Ma, coinciding with the Kaiman and Cretaceous Superchrons, respectively, and may be responsible for the Superchrons. The models predict vertical motion histories of the Slave and Kaapvaal cratons that are consistent with those inferred from thermochronology studies