As is well known, poor interfacial interactions between hydrophilic corn starch (CS) and hydrophobic thermoplastic matrices have been an obstacle in application of the quality biomass material like CS. The addition of compatibilizers is an effective method to improve the interface interaction. In this work, a special interficial structure using polyurethane crosslinked layer as compatible interface is designed and compatibilizers with different NCO functionality are also applied. The purpose of this work is to investigate the effects of compatibilizers with different NCO functionality (f, f = 0, 1, 2, 3) on the compatibility of corn starch-polycaprolactone (CS-PCL) composites. Subsequently, various CS-PCL composites are prepared using compatiblizers with different NCO functionality (f = 0, 1, 2, 3) via melting process. The structural analysis, mechanical properties, and water absorption capability as well as the thermal stability of the composites reveal that the properties of the composites are only enhanced significantly when the NCO functionality is no less than 2. In short, when f ≥ 2, a crosslinked layer could be formed at the interface of the composite to afford a compatible CS-PCL composite.