Abstract: Affected by both weakly stratified rock structures and groundwater conditions, water inrush disasters are prone to occur in weakly cemented and water-rich red-bed tunnels. Relying on the Longgang Tunnel of the Kaiyun Expressway, field tests and laboratory experiments are carried out to reveal the disaster-causing structural characteristics of water-bearing sections in the tunnel area, and the failure mechanical mechanism of weakly cemented red-bed rock mass. A three-dimensional discrete element Bonded Block Model (BBM)-fracture flow coupling model is established to analyze the evolution process of water inrush disaster in tunnels, investigate the influence of weakly cemented rock layer thickness and dip angle on the disaster, and evaluate the effectiveness of engineering control measures. The results show that: (1) Permeability failure tests indicate that seepage mainly occurs in rock fractures. (2) Water inrush is accompanied by fracture propagation and an increase in seepage rate in weakly cemented red-bed rock mass, and their interaction leads to the instability of surrounding rock at the tunnel face and a sharp drop in water pressure. (3) Rock layer thickness has a significant influence on surrounding rock instability and water inrush, while the influence of structural plane dip angle is relatively small. Under the condition of 0.3 m layer thickness, when excavation enters 3 m into the fractured zone, the water inflow reaches 954.2 m³/h, and the disturbance failure zone and seepage failure zone in front of the tunnel face reach 5.91 m and 3.14 m, respectively. (4) Drainage and pressure relief can effectively reduce water pressure at the tunnel face and inhibit seepage failure, and grouting reinforcement can improve rock mass strength and block seepage channels. The combined “drainage-grouting” control measure shows significant mitigation effectiveness.