The toughening modification of epoxy resin by polyurethane prepolymer (PU) can effectively solve the disadvantage of high brittleness in its application. In this study, a convenient way to toughen epoxy resins was explored, and the monomers PPG and MDI for the synthesis of polyurethane prepolymers were used for a one-step modification of epoxy resins. The test results of viscosity and elongation at break showed that P-M reduced the viscosity of the epoxy resin and improved the toughness. Especially when the content of P-M was 25%, the elongation at the break of the modified EP reached 196.56%. From a thermogravimetric and pyrolysis kinetic analysis, the P-M modification had better thermal stability than the PU modification. These findings have particular implications for the toughening and engineering applications of epoxy resins.