Pharmacosiderite Mo4P3O16 (Pharma-MoPO) consists of [Mo4O4] cubane unit and [PO4] tetrahedral to form an open framework with a microporous structure similar to that of LTA-type zeolite. Although attractive applications are expected due to its microporous structure and redox-active components, its physicochemical properties have been poorly investigated due to the specificity of its synthesis, which requires a high hydrothermal synthesis temperature of 360 °C. In this study, we succeeded in synthesizing Pharma-MoPO by hydrothermal synthesis at 230 °C, which can be applied using a commercially available autoclave by changing the metal source. Through the study of the solids and liquids obtained after hydrothermal syntheses, the formation process of Pharma-MoPO under our studied synthesis conditions was proposed. Advanced characterizations provided detailed structural information on Pharma-MoPO, including the location site of a countercation NH4+. Pharma-MoPO could adsorb CO2 with the amount close to the number of cages without removing NH4+. Pharma-MoPO exhibited stable catalytic activity for the hydrodesulfurization of thiophene while maintaining its crystal structure, except for the introduction of sulfide by replacing lattice oxygens. Pharmacosiderite Mo4P3O16 was successfully obtained by hydrothermal synthesis at a moderate temperature, and its microporosity for CO2 adsorption and catalytic properties for hydrodesulfurization were discovered.