Silicon is indispensable in semiconductor industry. Understanding its high-temperature thermodynamic properties is essential both for theory and applications. However, first-principle description of high-temperature thermodynamic properties of silicon (thermal expansion coefficient and specific heat) is still incomplete. Strong deviation of its specific heat at high temperatures from the Dulong–Petit law suggests substantial contribution of anharmonicity effects. We demonstrate, that anharmonicity is mostly due to two transverse phonon modes, propagating in (111) and (100) directions, and can be quantitatively described with formation of the certain type of nanostructured planar defects of the crystal structure. Calculation of these defects' formation energy enabled us to determine their input into the specific heat and thermal expansion coefficient. This contribution turns out to be significantly greater than the one calculated in quasi-harmonic approximation.