We have developed a model of lattice thermal conductivity in a freestanding three-layered Si/Ge/Si heterostructure. This model takes into account the phonon confinement and interface scattering. Moreover, we derive an analytical expression of the interface scattering rate for phonon conduction in a semiconductor heterostructure. It is found that the phonon transport is reduced in the heterostructure. We further investigate the dependence of the thermal conductivity of the Ge well layer on the Si barrier layer thickness. We show that the thermal conductivity of the well layer can be modulated in a wide range by adjusting the barrier layer thickness. It is found that the thermal conductivity of the well layer increases with the barrier layer thickness in the case of highly specular scattering. The obtained results can be used for tuning the thermal conductivity in nanostructures.