Being composed of alternating soft segments and hard segments, thermoplastic polyurethane (TPU) always displays complicated thermal behaviors on the heating scans, such as enthalpy relaxation, crystallization, recrystallization, and so on. The dynamics of enthalpy relaxation and the effect of phase separation and crystallization on enthalpy relaxation in TPU have been investigated by utilizing fast scanning chip calorimetry (FSC). Enthalpy relaxation takes place below T g , whereas crystallization occurs above T g . It turns out that the enthalpy relaxation exhibits either α-relaxation or β-relaxation behaviors at different temperature regimes as described by the Vogel−Fulcher−Tammann function or Arrhenius function, respectively. Isothermal annealing time dependency of T g illustrates that hard segments are embedded in soft segments in the molten state and represents the degree of phase separation as well. Moreover, FSC results combined with microbeam-small-angle X-ray scattering results elucidate that phase separation and crystallization can restrain chain motion and thus affect structural relaxation. With the same crystallinity, the system crystallized at low temperature has a more pronounced effect on decelerating enthalpy relaxation due to the larger specific surface area.