The compound ThGeO₄ can be stabilized in both the zircon and scheelite phases at ambient conditions. We have measured thermal expansion in both the phases of ThGeO₄ by high temperature X-ray diffraction experiments carried out up to 1273 K. We find that thermal expansion in scheelite phase is about 50 % more in comparison of the zircon phase. A transferable interatomic potential model is used for calculation of phonon spectra and thermal expansion in the two phases of ThGeO₄. The calculations are able to reproduce large difference in thermal expansion of the two phases of ThGeO₄ and enable microscopic understanding in them.