With the frequent occurrence of heavy rainfall weather, the accidents of lining cracking, water leakage, and instability failure of in-service karst tunnels are becoming more prevalent. The accumulation of high water pressure behind the lining due to surface rainfall recharge is the primary cause of hydraulic disasters in karst tunnels. Monitoring and early warning for in-service karst tunnels are crucial methods to prevent such disasters. Taking the karst tunnel of Zhengzhou-Wanzhou railway as an example, similar model tests and seepage numerical simulations were conducted to investigate the water pressure distribution behind the lining and the uplift displacement of the lining under different karst morphologies. The research results provide a reference for the operational monitoring and early warning control standards of karst tunnels. The results indicate that when the recharge of surface rainfall exceeds the drainage capacity of the tunnel, a hydrodynamic pressure system of "surface recharge + tunnel drainage" will form behind the lining, making the bottom of the invert prone to accumulating high water pressure. When there are karst cavities and dissolution fracture zones in the strata, surface rainfall will lead to localized increases in water pressure on the lining, causing it to bear eccentric loads and further deteriorating the stress on the invert. Using the water pressure and uplift displacement at the invert center as the control basis, the monitoring and early warning levels for karst tunnel operation are classified into normal operation, temporary repair, speed limit rectification, and closure for rectification. The research findings can offer insights for the structural design optimization and monitoring and early warning of karst tunnels.