To investigate the decrease of thermal conductivity (k) of nanoscale Si materials, we conducted the piezoelectric photothermal (PPT) method for the highly periodic Si nanopillar arrays embedded in Si0.7Ge0.3. The PPT is an electrode free method that can measure a heat propagation in the parallel to the nanopillars direction. A distinctive dip was observed in the frequency-dependent PPT signal intensity. By focusing the dip frequency, k was estimated from the comparison with the model analysis based on the one-dimensional multilayer thermal diffusion equation. The estimated k was 0.19 ± 0.07 W m-1 K, in the parallel to the nanopillars direction. Since the considerable decrease of k was confirmed from the non-radiative recombination point of view, we found the present non-destructive PPT method is very useful to estimate k in the nanostructured devices for the thermoelectric application.