As described in this paper, phosphonic-acid-containing double-decker-shaped polyhedral silsesquioxane (PHOS-DDSQ) was synthesized and the proton conductivity of the PHOS-DDSQ cast film was studied under humid and non-humid conditions. To synthesize PHOS-DDSQ, double-decker-shaped polyhedral silsesquioxane (DDSQ) was initially reacted with di(ethylene glycol) (DEG) vinyl ether using hydrosilylation reaction to attach four DEG units to one DDSQ (4DEG-DDSQ). Subsequently, a phosphate esterification of hydroxyl groups in 4DEG-DDSQ was carried out using POCl₃. NMR, XPS, and MALDI-TOF MS spectra and titration measurements revealed that the phosphate esterification connected two DEG units to form a crown-ether-like structure. This structure prevents hydrolysis of the phosphate ester bond. PHOS-DDSQ showed high thermal stability, with decomposition temperature exceeding 220 °C, because of its inorganic DDSQ core. A uniform film of PHOS-DDSQ can be fabricated by drop casting. The cast film showed high proton conductivity (0.12 S cm⁻¹) under humid conditions, which is comparable to that of a Nafion® membrane. Moreover, the cast film offered good proton conductivity under non-humid conditions (3.6 × 10⁻⁴ S cm⁻¹ at 170 °C). The conductivity and thermal stability indicate that PHOS-DDSQ is a good candidate for use as a proton-conductive membrane in hydrated type fuel cells as well as fuel cells operated at intermediate temperatures (100–200 °C) under non-humid conditions.