Two series of thermoplastic polyurethanes (TPUs), which used nitroester plasticiable tetrahydrofuran-ethylene oxide random copolyether as soft segment and adduction products of isophorone diisocyanate (IPDI) and toluene diisocyanate (TDI) with 1,4-butanediol as hard segments respectively, were successfully synthesized as binders for novel thermoplastic propellant. Mechanical tests and DSC techniques were applied to make characterizations of the polymers in order to choose candidate materials. Results shown that the TPU based on IPDI with fraction of the hard segment around 45% will meet requirements of propellant in terms of mechanical properties and glass transition of the soft segment phase. The results were further manifested in detail by quantitative studies of the degree of microphase separation as well as hydrogen bonding within the hard segment domain based on the equations established through FTIR and DSC analyses. It was found that mixing of two phases, which mainly referred to the mount of the hard segment dissolving into the soft segment phase, was as little as 10% in IPDI series TPUs, whereas it was almost up to 30% in TDI series. This indicated that better phase separation was achieved in IPDI series TPU. By contrast, studies of hydrogen bonding in domain revealed that the domain of TPUs prepared with TDI was much oriented in comparison with that with IPDI, which indicated higher processing temperatures. The results were raised by the melting index results under required conditions.