The Yellow River tunnel, located at 7 degree seismic region, is deeply buried in the reach where the swing of the riverbed is larger and siltation-erosion variation is severe. The tunnel is a discontinuously flexible structure composed of several hundreds rings. The key technique problem in the feasible scheme is the longitudinal deformation caused by erosion-siltation change and earthquake load. So the 3-D nonlinear finite element program is developed to analyze the longitudinal deformation, crack opening, dislocation etc.. According to the characteristics of the large scale model and many contact interfaces ， several approaches are adopted to control calculation scale and to ensure calculation precision, including rapid solution algorithm for the equations. The results show that the crack opening, the dislocation displacement, the bolt stress of span joints, and the concrete stress are all in the design permission range, and can satisfy the design requirement.