The study of multilayer Si/Mg$_{2}$Si structure in initial state and after thermal annealing in temperature range 50—750°C by the methods of small-angle X-ray diffraction and cross-section transmission electron microscopy is carried out. As-deposited silicide layers are amorphous. Magnesium silicide layers are amorphous with nanocrystalline inclusions of Mg$_{2}$Si in metastable hexagonal modification. After thermal annealing at T = 450°C, the Mg$_{2}$Si layers are crystallized with increasing in density and, correspondingly, with 7.3% reduction in period of the Si/Mg$_{2}$Si multilayer. The further annealing of Si/Mg$_{2}$Si multilayer results in crystallization of Si layers in temperature range 500—600°C. Consequently, period of the Si/Mg$_{2}$Si multilayer is decreased by 6.36%.