In this article, the structure and properties of the epoxy resin (EP) modified by polyurethane (PU) prepolymers were studied. The three types of polyurethane prepolymers, namely, polycarbonate-type PU (TPC), polyether-type PU, and polycarbonate-polyether-type PU were employed. The samples were analyzed by means of an infrared spectrometer, a differential scanning calorimeter, a scanning electron microscope, a transmission electron microscope, a scanning tunnel microscope, and a thermal gravimeter. The results show that the EP modified by TPC is of excellent thermal resistance and mechanical properties. Specifically, when the ratio of PU to EP is 10/100 (wt/wt), optimal properties are achieved.