Abstract: Water shortage has been much more serious in recent years in China, particularly with the need for national economic development. The long-distance water transfer and distribution projects have been constructed to increase the layout of the open channel behind the water transmission tunnels. Among them, the sluice gate has been one of the most important components for the water level and flow control structure in the water transfer projects. The precise control function is closely related to the water level-flow relationship during operation. In addition to the adjustment function, the sluice gate can also be implemented for the emergency closure of some canal sections under accident conditions. The traditional sluice flow relationship is experimentally obtained under the condition of upstream open flow. However, only a few studies were focused on the calculation of the flow relationship when the upstream free flow transitions to the unsteady flow state of the pressure flow. It is high demand for the precise regulation of the exit gates in a large number of long-distance water conveyance tunnels under construction. Otherwise, the water diversion project cannot safely and stably provide the demanded water to the irrigation areas and water-consuming units. Starting from the actual design parameters of the Water Transfer Project in the Central Yunnan Province of China, this study aims to establish a three-dimensional fluid mechanics model for the actual canal-tunnel system using numerical simulation, in order to explore the water open and full flow characteristics under the upstream boundary of the gate. A mathematical model of over-gate flow was also calculated suitable for the non-constant flow conditions. The simulation was verified from one- and three-dimensional perspectives. The simulation results show that the transition process basically conformed to the laws of hydraulics. The results show that: 1) There was a free-surface-pressurized flow upstream of the gate during the unsteady flow process in the sudden closure of the accident dispatch gate. The flow velocity of the open channel section behind the gate increased significantly during the transition, which was about twice the maximum flow velocity under the design flow condition. The pressure head appeared before the gate, where the maximum was about 33 m. 2) Once the average calibration error of the dimensionless formula reduced by 4 percentage points than before, there was a pressurized flow state in the upstream tunnel. The improved dimensionless formula was used to calculate the flow rate, while, the pressure head in the upstream tunnel of the gate was used to replace the upstream water level. 3) The maximum relative error of the unified calibration mode was 4.68%, indicating the acceptable accuracy range. Therefore, the improved formula presented a simple form to require the fewer calibration parameters. The calculation can provide a strong reference to set the inner boundary of the gate for the long-distance canal-tunnel system scheduling. The finding can also offer reliable technical and practical support for the safe and stable operation of the water transmission and distribution project.