The emergency control of Menglou~Qifang inverted siphon, which is about 72 km long, is the key to the safety of the Northern Hubei Water Transfer Project. Given the complicated layout of this project, traditional emergency control method has been challenged with the fast hydraulic transient characteristics of pressurized flow. This paper describes the application of model predictive control (MPC), a popular automatic control algorithm advanced in explicitly accounting for various constraints and optimizing control operation, in emergency condition. For the fast prediction to the pipe-canal combination system, a linear model for large-scale inverted siphon proposed by the latest research and the integrator-delay (ID) model for open canals are used. Simulation results show that the proposed MPC algorithm has promising performance on guaranteeing the safety of the project when there are sudden flow obstruction incidents of varying degrees downstream. Compared with control groups, the peak pressure can be reduced by 17.2 m by MPC under the most critical scenario, albeit with more complicated gates operations and more water release (up to 9.75 × 10⁴ m³). Based on the linear model for long inverted siphon, this work highlights the applicability of MPC in the emergency control of large-scale pipe-canal combination system.