Due to the mass consumption and engine thrust of a flexible missile during the powered phase flight, its natural vibration characteristics may be changed significantly. The calculation of natural frequencies and mode shapes plays an important role in the structural design of the missile. Aiming at calculating the natural vibration characteristics of the missile rapidly and accurately, a nonuniform beam subjected to an engine thrust is used to model the free vibration of the missile and Riccati transfer matrix method (RTMM) is adopted in this paper. Numerical results show that the natural frequencies of a typical single stage flexible missile are increased unceasingly in its powered phase, and its mode shapes are changed a lot. When the presented methodology is used to study the natural vibration characteristics of flexible missiles, not only the mass, stiffness, and axial compressive force distributions are described realistically but also numerical stability, high computation speed, and accuracy are achieved.