Lanthanide-based nanocrystals with heterogeneous core-shell structures possess elastic strain due to lattice mismatch and volumetric expansion or shrinkage. Strain relaxation is usually accompanied by lattice defects, especially those point defects and small defect clusters. However, the influence of strain on the formation of lattice defects remains unclear. Using OH- ions as a representative lattice impurity, first-principles calculations can be used to address the correlation between the thermodynamic stability of OH-based substitutional defects and elastic strain. Moreover, the concentration of OH- impurities in both strained and relaxed sodium yttrium fluoride lattices can be greatly reduced by increasing the concentration of fluoride-containing precursors. These findings suggest that minimal incorporation of OH- ions effectively suppresses multiphonon nonradiative relaxation and thus boost the efficiency of upconversion conversion.