The possibility of nanocrystal formation in silicon layers subjected to plasma-immersion helium-ion implantation at an energy of 5 keV has been proved for the first time. The effect of the implantation dose on the microstructure of the layers has been studied by X-ray reflectometry, transmission electron microscopy and Raman scattering. It has been established that the formation of silicon nanocrystals with dimensions of 10–20 nm is accompanied by a pronounced dependence on the ion flux and occurs at a dose of 5 × 10^17 cm^–2 with subsequent annealing at 700–800°C. The excessive dose has been shown to cause the destruction of the upper protective sublayer and the degradation of the optical properties of nanocrystals.