Polyurethanes (PUs) from Polyethylene glycol (PEG) and polycaprolactone diol (PCL) and a crosslinker, Pentaerythritol (PE), were synthetized with isophorone diisocyanate (IPDI). In this study, we investigated the effect of polyol and crosslinker composition on phase separation and thermo-mechanical properties. The properties were studied through dynamic mechanical analysis, X-ray scattering, atomic force microscopy (AFM), and thermogravimetric analysis (TGA). The results showed changes in PUs properties, microphase structure, and separation due to the composition of polyol/crosslinker blend. So, the largest concentration of PE produced multimodal loss factor patterns, indicating segment segregation while PUs with a PEG/PCL = 1 displayed a monomodal loss factor pattern, indicating a homogeneously distributed microphase separation. Additionally, the increase of the PEG concentration enhanced the damping capacity. On the other hand, agglomeration and thread-like structures of hard segments (HS) were observed through AFM. Finally, the thermal behavior of PUs was affected by chemical composition. Lower concentration of PE reduced the crosslinking; hence, the temperature with the maximum degradation rate.