Hypersonic vehicle can be designed into blended lift body by using light-weighted materials, which leads to close frequencies between controlled rigid-body motion and the oscillation of the structure. It brings about a huge challenge in the design of guidance and control system. Based on the assumed mode method, the free-free beam structural dynamics model considering variable cross-section effect was built. After comparing the mode shape and frequencies between cross-section and variable cross-section beam, it is found that the later one had a bigger mode shape change, and the frequency of second and three order both decreased. Given the hypersonic vehicle equations, the static and dynamic characteristics of constant cross-section and variable cross-section beam were analyzed in a typical condition. The results indicate that the variable cross-section beam has a larger appended angle of attack, the system is open-loop unstable, and exhibits non-minimum phase behavior in the trim condition.