Clathrates based on Si and Ge have very low lattice thermal conductivity (~1 W/m-K). This value can potentially be further reduced by alloying and nano-structuring. In this work, the thermal conductivity of Si and Ge clathrates alloy have been investigated using model based on the relaxation time approximation. By including alloy scattering, we find that the lattice thermal conductivity of Ba8Cu6Si40 is reduced by 50% from 1.64 to 0.80 W/m-K in Ba8Cu6Si40(1−x)Ge40x alloy. Further ~90% reduction of the thermal conductivity is possible for nanowire clathrate alloys. The ultra-low thermal conductivity in the nanowire will be very suitable for the thermoelectric application.