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Alkaline earth (AE) metal complexes have garnered significant interest in various functional fields due to their nontoxicity, low density, and low cost. However, there is a lack of systematic investigation into the structural characteristics and physical properties of AE‐metal‐organic frameworks (MOFs). In this research, we synthesized isostructural MOFs consisting of AE4(μ4‐Cl) clusters bridged by benzo‐(1,2;3,4;5,6)‐tris(thiophene‐2′‐carboxylic acid) (BTTC3−) ligands. The resulting structure forms a truncated octahedral cage denoted as [AE4(m4‐Cl)]6(BTTC)8, which further linked to a porous three‐dimensional framework. Among the investigated AE ions (Ca, Sr, and Ba), the Ca4‐MOF demonstrated good chemical stability in water compared to Sr4‐MOF and Ba4‐MOF. The N2 adsorption and solid‐state UV‐vis‐NIR absorption behaviors were evaluated for all AE4‐MOFs, showing similar trends among the different metal ions. Additionally, the proton conduction study revealed that the Ca4‐MOF exhibited ultra‐high proton conductivity, reaching 3.52×10−2 S cm−1 at 343 K and 98 % RH. Notably, the introduction of LiCl via guest exchange resulted in an improved proton conduction of up to 6.36×10−2 S cm−1 under similar conditions in the modified LiCl@Ca4‐MOF. The findings shed light on the regulation of physical properties and proton conductivity of AE‐MOFs, providing valuable insights for their potential applications in various fields. [ABSTRACT FROM AUTHOR]