To evaluate the deterioration problem of geometry and stress states for the ballastless track caused by the uneven subgrade settlement of high-speed railway，a 3D FEM model of the CRTS ΙΙ type ballastless track-subgrade system was established in this paper. A total of 64 types of differential settlements were simulated (with wavelengths of 5~40 m and amplitudes of 5~40 mm). Based on the flexibility of the concrete base，quantitatively characterizing method for the geometry mapping and stress level of the track structure was proposed. The results show that the mapping characteristics of the track structure are mainly determined by the flexibility of the concrete base. When the settlement wavelength is less than 15 m or the wavelength is between 15~20 m with the settlement amplitude greater than 15 mm，the subgrade and track are separated due to uncoordinated deformation. The increase of the track structure deformation leads to the development of additional tension stresses in the concrete structure and the subgrade contact stresses，which are prone to approach or exceed their allowable strength and results in damaged failure. Meanwhile，an increase of the modulus and thickness of the concrete base is not significant for improving the smoothness of the rail surface. On the contrary，it increases the track tensile stress and the subgrade contact stress.