It is critical to prepare ductile and hydrophobic modified starch material in an effective and environmentally friendly, way. In this work, polyurethane prepolymers (PUPs) with various isocyanates were synthesized and. mixed reactively with thermoplastic starches (TPS) in an intensive mixer to prepare modified TPS. The effects of the isocyanates on the structure and properties of the modified TPS were then investigated by using scanning electron microscope (ESEM); tensile tester, and contact angle meter. Results showed that mechanical properties of the modified TPS were improved with the increase in hydrophobicity of the isocyanate. 4,4'-Methylenedi-p-phenyl diisocyanate (MDI) was hydrophobic, the NCO groups in PUPs were not easily consumed by water when modified starch was prepared, leading to a significantly increased reaction of the NCO groups with As the amount of urethane bonds between starch and PUP increased, the compatibility between the two polymers was also improved, resulting in the improvement of tensile properties. Isocyanates played an important role in improving the compatibility between the starch and PUP and the properties of the modified TPS.