Abstract The substitution of Zn for Cu and Pr for Y in YBa 2Cu 3O 7− y has been studied extensively, and got some meaningful results. Most attention was paid to the change of carrier concentration on superconductivity. In this work, high-resolution X-ray diffraction, including Φ-scan and rocking curves, was used to study some small size single crystals of Zn- and Pr-doped YBa 2Cu 3O 7− y . It is discovered that the structural changes caused by the substitution of Zn for Cu mainly concentrate in the rock-salt block in the unit cell, i.e. the Cu(2)–O, Cu(1)–O, and Ba–O layers. But the structural changes caused by the substitution of Pr for Y distribute in the entire unit cell. Both the substitution of Zn and Pr decrease the value of T c of YBa 2Cu 3O 7− y . The effects of them were analyzed based on the structural change caused by substitutions. It is suggested that except the carrier concentration, structural change is an important factor to superconductivity.