The effect of thermal annealing on the multiple endothermic behavior and morphological changes in the silicon-containing and phosphorus-containing segmented polyurethane (Si-PU and P-PU) has been studied by differential scanning calorimetry (DSC). In the amorphous hard segments of the Si-PU and P-PU polymers that were annealed below T2, both the T1 temperature, and magnitude of T1 endotherm increased linearly as a function of the logarithmic annealing time (log t(alpha)). This result demonstrated that the endothermic behavior (T1 endotherm) is typical of enthalpy relaxation resulting from the physical aging of the amorphous hard segment. Furthermore, the P-PU polymer was unstable than the Si-PU polymer due to the fact that the phosphorus-containing hard segment produce aged more easily. Dissociation of domains and enthalpy relaxation of hard segments for the Si-PU polymer was associated with T2 endothermic behavior. However, the enthalpy relaxations of the T2 endothermic behavior for P-PU polymer was absent, which could be attribute to the behavior of degradation in the temperature range of T2 endotherm.