The phonon transport in the lateral direction for gap-controlled Si nanopillar/SiGe interlayer composite materials was investigated to eliminate heat generation in the channel area for advanced MOS transistors. The gap-controlled Si NP/SiGe composite layer showed 1/100 times lower thermal conductivity than Si bulk. Then, the phonon transport behavior in lateral direction could be predicted by the combination between 3-omega measurement method for thermal conductivity and Landauer approach for phonon transport in Si NP/Si0.7Ge0.3 interlayer composite structure. We found that the NP structure could regulate the phonon transport in the lateral direction by changing the NP gaps. As such, this structure achieves the first step toward phonon transport management in the same electron transportation direction of planar-type MOSFETs and represents a promising solution to heat generation for advanced CMOS devices.