SUMMARY One of the outstanding problems in modern geodynamics is the development of thermal convection models that are consistent with the present-day flow dynamics in the Earth’s mantle, in accord with seismic tomographic images of 3-D Earth structure, and that are also capable of providing a time-dependent evolution of the mantle thermal structure that is as ‘realistic’ (Earth-like) as possible. A successful realization of this objective would provide a realistic model of 3-D mantle convection that has optimal consistency with a wide suite of seismic, geodynamic and mineral physical constraints on mantle structure and thermodynamic properties. To address this challenge, we have constructed a time-dependent, compressible convection model in 3-D spherical geometry that is consistent with tomography-based instantaneous flow dynamics, using an updated and revised pseudo-spectral numerical method. The novel feature of our numerical solutions is that the equations of conservation of mass and momentum are solved only once in terms of spectral Green’s functions. We initially focus on the theory and numerical methods employed to solve the equation of thermal energy conservation using the Green’s function solutions for the equation of motion, with special attention placed on the numerical accuracy and stability of the convection solutions. A particular concern is the verification of the global energy balance in the dissipative, compressible-mantle formulation we adopt. Such validation is essential because we then present geodynamically constrained convection solutions over billion-year timescales, starting from present-day seismically constrained thermal images of the mantle. The use of geodynamically constrained spectral Green’s functions facilitates the modelling of the dynamic impact on the mantle evolution of: (1) depth-dependent thermal conductivity profiles, (2) extreme variations of viscosity over depth and (3) different surface boundary conditions, in this case mobile surface plates and a rigid surface. The thermal interpretation of seismic tomography models does not provide a radial profile of the horizontally averaged temperature (i.e. the geotherm) in the mantle. One important goal of this study is to obtain a steady-state geotherm with boundary layers which satisfies energy balance of the system and provides the starting point for more realistic numerical simulations of the Earth’s evolution. We obtain surface heat flux in the range of Earth-like values : 37 TW for a rigid surface and 44 TW for a surface with tectonic plates coupled to the mantle flow. Also, our convection simulations deliver CMB heat flux that is on the high end of previously estimated values, namely 13 TW and 20 TW, for rigid and plate-like surface boundary conditions, respectively. We finally employ these two end-member surface boundary conditions to explore the very-long-time scale evolution of convection over billion-year time windows. These billion-year-scale simulations will allow us to determine the extent to which a ‘memory’ of the starting tomography-based thermal structure is preserved and hence to explore the longevity of the structures in the present-day mantle. The two surface boundary conditions, along with the geodynamically inferred radial viscosity profiles, yield steady-state convective flows that are dominated by long wavelengths throughout the lower mantle. The rigid-surface condition yields a spectrum of mantle heterogeneity dominated by spherical harmonic degree 3 and 4, and the plate-like surface condition yields a pattern dominated by degree 1. Our exploration of the time-dependence of the spatial heterogeneity shows that, for both types of surface boundary condition, deep-mantle hot upwellings resolved in the present-day tomography model are durable and stable features. These deeply rooted mantle plumes show remarkable longevity over very long geological time spans, mainly owing to the geodynamically inferred high viscosity in the lower mantle.