This article deals with the synthesis of the SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> nanopowder in the original plasma system including a water-cooled reactor, arc plasma jet, and feed unit. The operating principle of this electro-plasma system is based on gas evaporation and condensation of the molten material. A continuous material feeding into the plasma jet provides the high yield of the target product due to a complete evaporation of the condensed phase. This article presents the experimental results of the SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> nanoparticle synthesis from high-silica natural material and the investigation of the particle phase composition after the conventional thermal treatment. It is found that the average particle size is about 100 nm at a maximum 25-kW power of the plasma jet; amorphized bonds in the synthesized high-dispersive powder provide the formation of polydisperse clusters of particles. The powder heating up to 1173 K results in crystallization and grouping of the SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> nanoclusters. The high-dispersive SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> powder allows stabilizing the phase transition to a modification of SiO <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$_{2}\alpha $ </tex-math></inline-formula> -tridymite that is not observed in the initial natural quartz.