Aiming at the water leakage in an underground interchange tunnel, the systematic analysis is carried out by comprehensive investigation and field test. And a structural automation health monitoring system is set up in key parts of the tunnel to observe and study the seasonal impact of external environmental temperature. The result shows that the main cause of pavement caustic soda and packing damage is the leakage of groundwater along the interlayer of the pavement at the deformation joints. The seasonal expansion and contraction deformation of tunnels will cause the deformation of expansion joints up to 10 mm. The blocking water between joints is the key to control the water leakage. By analyzing the disease factors, the composite modified asphalt based flexible grouting material is used to seal the deformation joints, and combined with a three-level scheme of water displacement, water blocking and water sealing, the groundwater leakage can be effectively solved. The research result can provide the reference for controlling the similar diseases.