In this work, polyurethane prepolymers (PUPs) with various NCO content proportions were synthesized and mixed reactively with a starch-water mixture to prepare modified thermoplastic starch (TPS) in an environmentally friendly way. The effects of polyurethane NCO content on the structure and/or properties of the modified TPS sheets were investigated. Results revealed that the reaction ratio of PUPs used for preparing the modified TPS was 99.8%, indicating that the PUPs were almost cross-linked to the starch matrix. With an increase of NCO content in PUP, the tensile strength of the modified TPS increased from 19.3 to 37.4 MPa, and the elongation from 1.7% to 17.2%. As the PUP's NCO content increased, the amount of urethane linkage between PU microparticles and the starch matrix would increase. In addition, the compatibility of the two polymers was also improved resulting in the improvement of tensile properties. The urethane linkage between PU and starch therefore played an important role in improving the toughness of the modified TPS.