Elastic strain engineering is an important strategy to design material properties in semiconductor and emerging advanced manufacturing industries. Recently, peak-pair method has drawn great attention compared to geometric phase analysis, owing to its precise determination of atom position at real space. Most current strain characterization methods estimate the local strain by comparing it with the related information from unstrained areas as reference. However, peak-pair method generated large errors in some cases because of the complexity of lower symmetric crystal structures, such as hexagonal structure. In this study, we introduce a new algorithm to overcome this limitation by directly comparing the atom positions with multiple references with different lattice symmetries. Furthermore, this new method is validated through several complicated crystal systems such as hexagonal, orthorhombic, monoclinic, and tetragonal structure, and returns expected values. This finding is essential to reliably determine the localized elastic strain with various crystal structures.