Nanostructured semiconductors open the opportunity to independently tailor electric and thermal conductivity by manipulation of the phonon transport. Nanostructuring of materials is a highly promising strategy for engineering thermoelectric devices with improved efficiency. The concept of reducing the thermal conductivity without degrading the electrical conductivity is most ideally realized by controlled isotope doping. This work reports on experimental and theoretical investigations on the thermal conductivity of isotopically modulated silicon nanostructures. State-of-the-art pump-and-probe experiments are conducted to determine the thermal conductivity of the different nanostructures of isotopically enriched silicon layers epitaxially grown on natural silicon substrates. Concomitant molecular dynamics calculations are performed to study the impact of the silicon isotope mass, isotope interfaces, and of the isotope layer ordering and thickness on the thermal conductivity. Engineering the isotope distribution is a striking concept to reduce the thermal conductivity of silicon without affecting its electronic properties. This approach, using isotopically engineered silicon, might pave the way for future commercial thermoelectric devices.