Polytype nanowires fabricated in both silicon and germanium are particularly attractive for thermoelectric engineering. In this work, the transport of phonons across polytype heterojunctions such as Si 3C/Si 2H and Ge 3C/Ge 2H is theoretically studied by using a particle Monte Carlo simulation for phonons. Full‐Band dispersions and phonon‐phonon scattering rates are calculated by using the density‐functional theory. Phonon transmission across interfaces is implemented by using a Full‐Band version of the Diffusive Mismatch Model. First, the different transport regimes (diffusive, ballistic, and intermediate) for homogenous 3C and 2H Si and Ge bars are investigated by using the Knudsen number as well as the spectral contributions of the thermal flux. Then, single and double polytype Si and Ge heterostructures are studied. The variation of the interface thermal conductance as a function of the geometric dimension as well as the effects of the spectral distribution of the flux are investigated. This local indicator of the phonon transport regime can be used as a local indicator of the occurrence of the out of equilibrium transport regime. Finally, it is shown that the polytype interfaces exhibit significant thermal resistances and generate an out of equilibrium phonon transport regime around the interface over several nanometers.