Abstract: A comprehensive research approach integrating field measurements, theoretical analysis, numerical simulation, and engineering practice is adopted to address roadway roof instability and water inrush during excavation under a confined aquifer. The instability mechanisms of roadway roofs with a thin aquifuge and the key prevention and control technologies are systematically investigated. The results indicate that water inrush disasters in roadway roofs require the simultaneous presence of three fundamental conditions: a water source in the aquifer, stable water supply conditions, and through-going fractures formed by the coupling of engineering disturbances and hydro-mechanical effects.Based on an elastic–plastic roof beam model, a theoretical formula for calculating the height of the plastic zone in the roof is derived. This reveals that the plastic zone height expands with increasing roadway burial depth and cross-sectional width, and highlights the significant influence of the internal friction angle of the surrounding rock on plastic zone development. A mechanical model of the surrounding rock, considering different aquifuge thicknesses, is established through numerical simulation, and the effects of aquifuge thickness on stress distribution, displacement response, and plastic zone extension are systematically analyzed. Simulation results show a critical threshold (5.0 m) for aquifuge thickness. When the aquifuge thickness falls below this threshold, roof displacement exhibits a nonlinear, sharp increasing trend, the plastic zone in the surrounding rock rapidly expands and eventually penetrates the aquifuge, forming a water-conducting channel connected to the upper aquifer, thereby significantly increasing the risk of water inrush.Based on the mechanistic findings, a comprehensive control strategy centered on “drainage and pressure reduction” and “dynamic reinforcement support” is proposed. Specific measures include: constructing upward-inclined drainage holes in the roadway sides to actively relieve roof water pressure and reduce the softening and splitting effects of water on sandy mudstone; and concurrently implementing a synergistic support system of “zonal support – layered grouting – frame support” to dynamically reinforce the roof bearing structure. Grouting reinforcement is primarily applied to the shallow fractured rock mass to enhance the integrity and cohesion of the surrounding rock. The support system flexibly selects structures such as anchor cables, steel straps, and I-beam frames based on the relationship between the plastic zone and aquifuge thickness, achieving the control objective of “combining blockage and drainage, integrating consolidation and support”. Field applications demonstrate that this comprehensive control strategy effectively manages surrounding rock deformation and roof water inrush, ensuring safety and stability during roadway excavation. This study not only reveals the intrinsic mechanisms of roof instability and water inrush under thin aquifuge conditions, but also provides theoretical foundations and practical references for water hazard prevention and roof stability control in roadway engineering under similar hydrogeological conditions.