Alkaline earth metal cations are ubiquitously present in natural zeolites but less exploited in synthetic zeolites due to their low solubility in water, and hence it remains elusive how they contribute to zeolite formation. Herein, harmotome, a PHI-type zeolite with Ba2+, is readily synthesized from a Ba-containing aluminosilicate glass. This glass-to-zeolite transformation process, in particular the structure-regulating role of Ba2+, is investigated by anomalous X-ray scattering and high-energy X-ray total scattering techniques. The results demonstrate that the steady Ba2+-aluminosilicate interactions not only help prevent the precipitation of barium species under alkaline synthetic conditions, but also dictate the local structures with distinct interatomic distances between the Ba2+ and the surrounding aluminosilicate species throughout the transformation process, which lead to the successful formation of harmotome without detectable impurities. This study highlights the usefulness of the comprehensive X-ray scattering techniques in revealing the formation scheme of the zeolites containing specific metal species. In addition, a promising alternative approach to design and synthesize zeolites with unique compositions and topologies by using well-crafted glasses with suitable metal cation dopants is demonstrated.