The dual-modes phenomenon， which means the direction of the missile modal vibration deviates greatly from the quadrant direction， appears in the missile modal experiment. A combined finite element model of shell-beam-mass-spring element is constructed for simulating missile modal test system by using the three-section method. By the experimental analysis and simulation verification， the main reason of the dual-modes is proved. The connection stiffness direction of the joint surface between cabins deviates from the quadrant direction. Furthermore， two conclusive cognitions affecting the missile modal characteristics are presented according to the experimental results， and two preconditions for the deviation of the modal direction from the quadrant direction are obtained with the help of simulation results. Finally， from the engineering application view point， operation instructions of modal parameters are provided， and the design and location of the joint surface between cabins are presented. Results of this paper are of great importance to the avoidance and weakening of missile dual-modal phenomenon.