The water absorption and expansion characteristics of the swelling surrounding rock can have adverse effects on the tunnel lining structure, which can easily lead to the induction of various engineering disasters, and impact the progress of the project, as well as the normal operation of the train in subsequent stages. Therefore, the mechanical characteristics and support method selection of such tunnels have always been of great concern. Taking a tunnel passing through expansive mudstone in Inner Mongolia as an example, based on field monitoring and numerical calculation methods, the deformation and failure characteristics of the tunnel lining structure in mudstone tunnel under the original lining conditions were analyzed. Subsequently, the applicability of double-layer preliminary lining in such tunnels was studied from the aspects of support deformation and mechanical properties, and corresponding lining parameter suggestions were proposed. The results indicate that the expansion of mudstone causes the deformation of the original lining structure (single-layer preliminary lining) to reach a magnitude of 309 mm. Such deformation leads to significant encroachment of the lining and necessitated forced arch replacement during the tunnel construction process. In comparison to the single-layer preliminary lining, the double-layer preliminary lining construction method has been found to significantly improve the deformation and stress state of the tunnel in expansive mudstone, achieving a deformation reduction rate that exceeds 63.88%. As the thickness of the secondary preliminary lining increases, the deformation and stress of the preliminary lining gradually decrease, achieving a maximum deformation reduction of 234.5 mm and a compressive stress reduction rate of up to 39% under various conditions. Consequently, the double-layer lining construction method can be considered for tunnels in expansive mudstone, with the thickness of the secondary preliminary lining being reasonably selected based on deformation requirements. The research findings can serve as a valuable reference for similar projects in the future.