A method of manufacturing an SOQ substrate and an SOQ substrate manufactured by the same are disclosed. In the method, hydrogen ions are implanted to a surface of a single crystal Si substrate through an oxide film to uniformly form an ion implanted layer at a predetermined depth from the surface of the single crystal Si substrate, and a bonding surface of the substrate undergoes a plasma treatment or an ozone treatment. An external shock is applied onto the single crystal Si substrate and quartz substrate, which are bonded together, to mechanically delaminate a silicon film from a single crystal silicon bulk. In this way, the SOQ film is formed on the quartz substrate through the oxide film. To further smooth the SOQ film surface, hydrogen heat treatment is performed at a temperature of 1000° C. or less below a quartz glass transition point.