Silicon quantum dots (SiQDs) with a mean diameter of 3.9 nm, smaller than the excitonic Bohr radius of silicon, were obtained using a simple and low-cost high temperature decomposition method using Si and O as starting elements without the addition of dopants, surfactants and ligands. These SiQDs were embedded in a highly oriented and fairly long amorphous silica wire array with a diameter of 500 nm and length up to 2.5 mm. The corresponding Raman peak of the as-prepared products was downshifted and asymmetrically broadened, which was attributed to the effect of phonon confinement and may be quantitatively verified with the diameter distribution of SiQDs using a theoretical method. The pure SiQDs, emitting photoluminescence of 800 and 1550 nm at room temperature, were only covered with silica, which may serve as a model to investigate the nature and emission mechanism of SiQDs. These visible and infrared emissions would originate from the intrinsic defects in the SiQDs, suggesting opportunities for developing cheap and novel types of silicon-based optical and waveguide devices in the future.