Ionic polyurethane (PU) membranes of hydroxyl-terminated polybutadiene (HTPB) and 4,4＇-dicyclohexylmethane diisocyanate (H12MDI) were polymerized by a two-stage method. The ionic group was introduced by adding N-methyldiethanolamine (MDEA) as the chain extender of which the tertiary amines were complexed with cobalt ions. It was found that the binding of hard segments and the flexibility of soft segments had subtle effects on the gas permeability. The effects of hard segment content and the amount of cobalt ion on the gas permeability and morphological properties were investigated. Fourier transform infrared (FTIR) spectroscopy was utilized to identify the segregation between hard and soft segments and structure change, which affect the transport properties. The hydrogen bonding index (HBI), frequency difference, and shift as a measure of the phase segregation and the average strength of the interpolymer hydrogen bonds were utilized to study the intermolecular interaction and transport property of the prepared PUs. The results of differential scanning calorimetry, thermogravimetric analysis (TGA), and FTIR measurements explain the complexation and, hence, the gas permeability.