A fundamental investigation of the influence of novel phosphonium bromide salts within the polymer main chain (23.75 mol %) of polyurethanes was conducted to elucidate the effect of ionic associations on hard segment hydrogen bonding. A novel poly(tetramethylene oxide) (PTMO)-based polyurethane containing a phosphonium diol chain extender was prepared using a conventional prepolymer method. In addition, a polyurethane containing a 1,4-butanediol chain extender was synthesized for comparison with the thermomechanical and morphological properties of the phosphonium ion-containing analog. Moreover, the unprecedented comparison of morphological development in the presence of cationic sites is described herein. Differential scanning calorimetry (DSC) revealed that phosphonium polyurethane was more crystalline compared to the noncharged analog, and it was presumed that enhanced hydrogen bonding in the noncharged polyurethane restricted polymer mobility and reduced PTMO crystallinity. Moreover, FT-IR spectroscopy demonstrated that hydrogen-bonding interactions were significantly reduced in the presence of phosphonium cations. These results correlated well with tensile properties, i.e., the noncharged polyurethane offered superior tensile strength compared to phosphonium polyurethane. X-ray scattering indicated that both polyurethanes were amorphous at room temperature and exhibited hard segment microphase separation. Upon stretching, the interparticle scattering between the microphase-separated domains aligned preferentially along the stretching direction. Scanning transmission electron microscopy (STEM) and energy-dispersive X-ray spectroscopy (EDS) in the STEM indicated that the charged polyurethane exhibited ionic aggregates that were rich in P and Br.