To explore the mechanism of pavement arching disease in phyllite soft rock tunnels and propose targeted disease treatment measures, based on the Yunling Tunnel in the Shiyan?Manchuanguan section of the Fuzhou?Yinchuan Expressway, typical tunnel diseases were investigated, and triaxial compression tests of phyllite in natural and saturated states were conducted to study the failure laws of the tunnel under the combined action of fault fracture zones and groundwater. The research results indicate that the compressive strength and elastic modulus of the rock in the saturated state are lower than those in the natural state, which demonstrates that the structure of phyllite undergoes damage and deterioration after being exposed to water. The fault penetrates the tunnel in an inclined manner, resulting in the phenomenon of unsymmetrical loading in the tunnel. A larger permeability coefficient of the fault means a larger volume of the plastic zone. Under the seepage?stress coupling effect of the tunnel, groundwater and faults reduce the bearing capacity and shear resistance of the surrounding rock at the tunnel bottom, leading to pavement arching in the tunnel. Starting from improving the integrity and bearing capacity of the surrounding rock and lining structure, three categories and six types of disease treatment schemes were proposed for different disease causes and degrees. A new technology of embedded arch reinforcement structure was proposed for sections with severe pavement arching. The on-site construction effects show that the treatment and reinforcement achieve the expected effects, with good economic and social benefits.