In this chapter we present a review of the phonon thermal conductivity of segmented nanowires focusing on the theoretical results for Si and Si/Ge structures with the constant and periodically modulated cross-sections. We describe the use of the face-centered cubic cell and Born-von Karman models of the lattice vibrations for calculating the phonon energy spectra in the segmented nanowires. Modification of the phonon spectrum in such nanostructures results in strong reduction of the phonon thermal conductivity and suppression of heat transfer due to a trapping of phonon modes in nanowire segments. Possible practical applications of segmented nanowires in thermoelectric energy generation are also discussed.