In order to analysis the influencing extent of structural vibration effects on fatigue life, a methodology of vibration fatigue analysis was presented based on rigid-flexible coupling simulation. With the Interface Transaction Technical Strategy (ITTS) for flex-body, the model of rigid-flexible coupling system is established, in which the flex-body can produce the elastic vibration characterized by the relevant modal vibrations under the dynamical constraint interactions. By the Component Modal Synthesis (CMS) approach of stress recovery, the following analyses are carried out to determine the fatigue quality and the influencing extent of vibration: the correlation between dynamical stress and modal vibration, and the stress range histograms by which the amplitude and number of cycle stress on critcal points are contrasted stastically among the multi-condition. For the vertical vibration problem of container flatcat, for instance, vertical acceleration on high side, it is sured that under the dynamical interaction of the wedge’s stick-slip friction, the flatcar produces the elastic vibration characterized by the 2nd vertical bending modal, which can be validated by both modal mass and attached mass models of flatcar. According to the modal correlation analysis and the statistical contrast of stress range histogram for the cycle stress on crotical points, the vertical and lateral constraint forces of container feets are one of the main causes of the large amplitude of cycle stress on critcal points, and the influencing extent of structural vibration on fatigue life is up to (20-25)%.