Isotopically modulated silicon and germanium multilayers are analyzed by means of femtosecond spectroscopy and pulsed X-ray scattering for determining thermal conductivity and phonon modes. Isotopic modulation decreases thermal conductivity stronger than expected from a band bending model in the coherent phonon transport regime, in particular for silicon. Femtosecond spectroscopy and X-ray scattering resolve zone-folded vibration modes, which are located at the edge of the new, smaller Brillouin zone due to the multilayer periodicity. These modes can contribute to the reduction of thermal conductivity by Umklapp processes within the zone-folded mini-bands. Color-coded increase in ultrafast X-ray scattering in vicinity to the mini-zone boundary of a germanium multilayer.