The periodic nanostructuring of inner part of semiconductors can be successfully accomplished by the infrared ultrashort pulse laser with a double pulse configuration. Self‐organized nanostructures inside semiconductor could be induced empirically only if it is indirect band gap semiconductor. The strained silicon regions with a width of about 100 nm are self‐aligned parallel to the polarization direction of the first arriving pulses, despite of the polarization direction of the secondly arriving pulses. AFM inspections reveal that such strained silicon nanostructures exhibit high electric conductivity and low thermal conductivity. The formation mechanisms would be interpreted in terms of the electrostrictive force through the interaction between electron‐hole plasma and phonon. Apart from the basic understanding, such nanostructured silicon will open the door to the fabrication of the self‐contained thermoelectric devices.