The fine structure of YBa2Cu3Oy single crystals with a different oxygen content subjected to a low-temperature hydrogenation have been investigated by transmission electron microscopy. It has been shown that as a result of the action of hydrogen at T = 150°С, a partial reduction of copper occurs, accompanied by the precipitation of Cu crystallites of ~100 nm in size and the formation of various structural defects. The geometric configuration of the precipitated crystallites has been considered. The results obtained show that hydrogenation is a method that makes it possible to control the structure by introducing nanosized inclusions and defects, which can be pinning centers of the magnetic vortices.