The features of the structure of nanorystalline Ce1-xPrxO2-y system (0 ≤ × ≤ 0.5) prepared via a complex polymerized precursor (Pechini) route have been elucidated by using a combination of spectroscopic (XANES, XPS) and structural (TEM, neutron diffraction) methods. Within the studied range of composition, the structure of all samples air annealed at 500 °C corresponds to single-phase fluorite-like solid solution. The relative content of Pr3+ both in the bulk and in the surface layer appears to be as high as 20–50%. The Rietveld refinement revealed non-monotonous variation of structural parameters (lattice parameter, domain size, microstrain density, Ce-O and O-O distances) and residual lattice hydroxyls concentration with Pr content. Clustering of defects along with variation of the mean Pr cation radius/charge state and disordering of the surface layer/ domain boundaries appear to be responsible for the observed features.