Magnesium (Mg) alloys with long-period stacking ordered (LPSO) phases are receiving increasing interest because of their excellent mechanical performance. The close similarity in atomic stacking sequences between different LPSO polytypes and Mg lattice often leads to ambiguous indexing in electron backscatter diffraction (EBSD), a commonly used material characterization technique. Instead of the Hough transformation approach used in commercial software, an alternative indexing approach, which can catch subtle differences by matching experimental patterns with simulated ones, is explored in this study. Our results, showing ~94% of mapping data being correctly indexed as the target phase, 14H LPSO, demonstrate the capability of not only resolving the LPSO phases but also distinguishing different LPSO polytypes. This approach offers a valuable, if not unique, solution for the microscale characterization of LPSO phases, enabling precise microstructure tuning to further promote the mechanical properties of Mg alloys.