The missile for this study has shown different natural frequency characteristics depending on the test conditions; natural frequencies obtained from its flight test are higher than those in its ground test. It was found that the hinged joints connecting front airframe to rear one had the nonlinear stiffness and caused the missile to show very complex dynamic characteristics. The angular stiffness at hinged joints was calculated using 3D finite element analysis, and it was verified that there was a highly nonlinear relationship between angular stiffness and external load. Natural frequencies calculated considering the nonlinearity of angular stiffness were nearly the same as test results. Through this study, the dynamic characteristics of a missile having split airframes with hinged joints could be clearly identified and a way of maintaining its natural frequencies consistent was generated.