We report on theoretical investigation of phonon thermal transport in Si/Ge and Si/SiO2 crosssection modulated nanowires. The calculations of the acoustic phonon energies were carried out in the framework of the face-centered cubic cell and Born von Karman models of the lattice dynamics [1-2]. The thermal conductivity was calculated in the framework of Boltzmann transport equation approach within the relaxation time approximation. The significant suppression (up to an order of magnitude, see Fig. 1) of the thermal flux in Si/Ge and Si/SiO2 cross-section modulated nanowires (MNWs) in comparison with generic silicon nanowires (NW) is established. Modulation of nanowire cross-section leads to suppression of the thermal flux and decreasing the phonon group velocities due to the redistribution of the phonon spectrum. Acoustical mismatch of materials and narrow segments of nanowires are responsible for appearance of the phonon modes, localized in nanowire segments. These modes possess low group velocity and weakly participate in the thermal transport. Low values of the thermal flux and thermal conductivity of cross-section modulated nanowires make them prospective for thermoelectric applications.