To make clear the physical mechanism of substitution by the magnetic ions Fe and Ni in different sites in YBCO systems, the positron annihilation technology (PAT) and simulated calculations are utilized to systemically investigate the compounds YBa2Cu3-x（Fe，Ni）xO7-δ（x=0.0—0.5）. The results obtained show that the doping ions Fe and Ni form different kinds of ion clusters and enter the crystal lattice. When occupying Cu(2) sites in CuO2 planes, the ions gather into double square and/or other clusters, which results in a strong electronic localization and would directly affect the pairing and transportation of carriers, so the superconductivity is suppressed dramatically. While ions substitution for Cu(1) through gathering hexamer and/or other clusters, this induces the localization of holes and weakens the function of carrier reservoir; thus carriers cannot easily transfer to CuO2 planes. However, in this case, the pairing and transportation of carriers are not affected directly, thus the superconductivity will be suppressed weakly. On the other hand, the present results indicate the suppression of superconductivity has no direct correlation with the magnetism of Fe and Ni ions itself.