Abstract: The swelling of clay mineral-rich mudstones upon water exposure is a critical factor contributing to various geological hazards. However, there remains a lack of in-depth investigation into the microscopic and macroscopic response mechanisms of clay minerals during the swelling process of mudstones, particularly at the molecular scale. This study employs salt ions are as a ‘probe,’ integrating experimental methods and molecular dynamics simulations to investigate the role of key interfaces in controlling the swelling process of mudstone under water immersion. Results indicate that the formation of numerous internal cracks within the mudstone is the primary cause of its swelling and deformation. The addition of salt ions exerts a similar inhibitory effect on both the swelling and water absorption of the mudstone. At the molecular level, simulations reveal that salt ions suppress the interlayer expansion during the hydration process of montmorillonite, highlighting the crucial role of montmorillonite in mudstone swelling. In contrast, illite resists hydration swelling due to strong interlayer interactions and the formation of a boundary hydrogen-bond network. Furthermore, two interfacial response mechanisms underlying mudstone swelling and deformation are elucidated: (1) hydration of intramolecular interlayer interfaces of montmorillonite, which generates structural cracks through crystalline expansion within dense agglomerates; and (2) infiltration at intermolecular micropore and crack interfaces, leading to air compression within the mudstone, which causes primary crack expansion and the formation of a crack network. This study provides a foundation for advancing the understanding of catastrophic processes associated with water-related mudstone strata.