In this study, polycaprolactone (PCL)‐based polyurethane prepolymers (PCLPU) with different types of hard‐segments were used as compatibilizers to prepare compatible starch‐PCL composites in an intensive mixer. The effects of the hard‐segments in the PCLPU compatibilizers on the structure and properties of the compatible starch‐PCL composite were analyzed thoroughly. The results showed that the addition of the PCLPU compatibilizer to the composites successfully improved the compatibility between starch and PCL. Also, since the NCO content of the different PCLPU compatibilizers was similar, the major factor that affected the structure and properties of the compatible starch‐PCL composites was the difference in the interactions between the PCL matrix and the different PCLPU compatibilizers. The physical crosslinking between the PCL matrix and the PCLPU with aromatic diisocyanate‐based hard‐segments was stronger than that between the PCL matrix and the PCLPU with aliphatic diisocyanate‐based hard‐segments due to the smaller degree of phase separation that occurred in the PCLPU with aromatic diisocyanate‐based hard‐segments. Additionally, analyses of the emission scanning electron microscopy (SEM), differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), wide‐angle X‐ray diffraction (WAXRD), and mechanical testing results of the composites showed that the compatibility between the starch and the PCL was improved significantly by the existence of the strong physical cross‐linking between the PCLPU compatibilizer and the PCL matrix. Toward this end, the PCLPU with aromatic diisocyanate‐based hard‐segments improved the compatibility between the starch and the PCL better than the PCLPU with aliphatic diisocyanate‐based hard‐segments, and thereby boosted the overall performance of the composite materials to a higher degree.