Complex crystal symmetry variation is observed for the oxygenated PrBa2−xLaxCu3O7+y system (0⩽x⩽1, −0.12⩽y⩽0.39). Powder X-ray Rietveld analysis indicates that the crystal structure changes from the PrBa2Cu3O7 or CuBa2PrCu2O7 1212C-type (C for chain) orthorhombic O(I)-phase (space group Pmmm) to 1212-type tetragonal T-phase (P4/mmm) around x=0.45, and then to a new 1212-type of orthorhombic O(II)-phase (Cmmm) around x=0.65. However, regardless of the structural change, anomalous Pr ordering temperature TN(Pr) decreases monotonically from 18 K for PrBa2Cu3O6.88 to 2.8 K for PrBa1.3La0.7Cu3O7.24. The increasing Pr–O bond length with decreasing TN indicates that Pr ordering is closely correlated with the wave function overlap between Pr–4f orbital and O–2pπ orbital in the CuO2 bi-layers.