Based on the pre-development general characterization model of track structure deformation and the evolution of interlayer interface state induced by the deformation of high-speed railway foundation, the description function of cosine subgrade settlement was implanted, and the Heaviside function was introduced to describe the contact nonlinearity between track and subgrade, the deformation equation of each layer of longitudinally connected ballastless track under cosine subgrade settlement was derived, the progressive approximation method was used to solve hyperstatic equation with contact nonlinearity, and the influence law of cosine subgrade settlement on the track structure deformation of each layer and the evolution of interlayer interface state was analyzed. Results indicate that: in the cosine subgrade settlement area, the track deforms accordingly with the subgrade settlement, when the subgrade settlement wavelength is constant, the track settlement and heaving increase with the increase of the subgrade settlement amplitude, when the settlement amplitude is constant, the track settlement increases with the increase of the subgrade settlement wavelength, but the track heaving decreases. The void area between track-subgrade and the track force curve are symmetrical, and the track overall stiffness affects the void length and height. When the subgrade settlement wavelength is 10m, with the increase of the subgrade settlement amplitude, the void height and length increase, it will also shift away from the settlement area as a whole. When the subgrade settlement amplitude is 10mm, it is necessary to focus on the uneven settlement with settlement wavelength less than 20m.