To clarify the water-sensitive deterioration mechanisms of red-bed soft rocks under repeated wetting–drying cycles, mudstone samples from two representative sites in the Sichuan Basin were investigated through multiscale experiments combining mechanical testing, X-ray diffraction (XRD), and scanning electron microscopy (SEM). The results showed that samples from Sampling Site ① exhibited higher compressive strength, elastic modulus, cohesion, and friction angle due to stronger cementation and greater structural integrity, whereas samples from Sampling Site ② showed weaker bonding and more initial structural defects. During wetting–drying cycling, both rock types experienced progressive mechanical degradation, with elastic modulus exhibiting the most pronounced deterioration after eight cycles. XRD analysis indicated that the main mineral assemblages remained stable without obvious phase transformation, while the reduction in calcite and clay minerals was associated with the weakening of cementing materials. SEM observations revealed distinct deterioration pathways: Site ① mainly underwent gradual damage characterized by particle-contact weakening, pore development, and shrinkage cracking, whereas Site ② experienced rapid structural degradation involving cement dissolution, particle debonding, and pore–fracture connectivity. These results indicate that wetting–drying deterioration is governed not only by mineral composition but also by bonding conditions and initial pore–fracture structures. The findings provide insights into the differentiated stability assessment and prevention of red-bed soft rock slopes and subgrades under water-sensitive environments.