Thermoplastic polyurethanes (TPUs) are versatile polymers presenting a broad range of properties as a result of their countless combination of raw materials—in essence, isocyanates, polyols, and chain extenders. This study highlights the effect of two different chain extenders and their combination on the structure–property relationships of TPUs synthesized by reactive extrusion. The TPUs were obtained from 4,4-diphenylmethane diisocyanate (MDI), polyester diols, and the chain extenders 1,4-butanediol (BDO) and dipropylene glycol (DPG). The BDO/DPG ratios studied were 100/0, 75/25, 50/50, 25/75, and 0/100 wt.%. The TPUs were characterized by size exclusion chromatography (SEC), Fourier-transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC), small-angle X-ray scattering (SAXS), UV–vis spectroscopy, and physical-mechanical properties. The results indicate that DPG promotes compatibility between rigid (HS) and flexible (SS) segments of TPUs. Consequently, increasing DPG content (>75 wt.%) reduced the organization of the rigid segments and the degree of phase separation, increasing the polydispersity of the interdomain distance and the transparency in the UV–visible spectrum of the TPUs. Furthermore, increasing DPG content also reduced the amount of hydrogen bonds present in the rigid phase, reducing or extinguishing its glass transition temperature (TgHS) and melting temperature (Tm), and increasing the glass transition temperature of the flexible phase (TgSS). Therefore, increasing DPG content leads to a deterioration in mechanical properties and hydrolysis resistance.