In this work, polyurethane prepolymers (PUP) were synthesized using different weight-average molecular weight (M-w) of poly-1,4-butylene glycol adipate (PBA), and then used to prepare modified thermoplastic starch (TPS) in an intensive mixer. The effects of M-w of polyurethane soft segments on the structure/properties of the modified starch sheets were investigated. Results showed that the reaction ratio of PUP used for preparing the modified TPS was 96.7%, indicating that PUP was almost crosslinked to starch matrix and the special structure of microparticles with multifunctional groups was essential to increase the reaction efficiency of modifiers during the solid modification. With the decreasing molecular weight of soft segments in PUP, the NCO content of PUP would increase, and the compatibility of the two polymers was also improved due to increasing number of urethane bonds between starch and PU, resulting in the improvement of breaking elongation. A similar trend was also observed by WXRD. Therefore, the relatively low molecular weight of PUP was beneficial for improving the miscibility of the modified starch materials.