The water conveyance tunnel is an important hydraulic structure in water conservancy projects. Typically, it manifests as a non-prismatic tunnel due to variations in the cross-sectional geometry, which give rise to an unpredictable flow pattern that significantly impacts the secure and stable operation of the tunnel. This study takes water conservancy project X as a case and investigates the hydraulic performances of a non-prismatic water conveyance tunnel using a scale model test and numerical simulation; the hydraulic performance, such as flow pattern, discharge, flow velocity, and water depth profile are analyzed for both free flow and submerged flow conditions. The results show that the simulation data fit well with the experimental value observed in the scale model test for free flow; however, a substantial discrepancy emerges under submerged flow conditions. This discrepancy is attributable to the presence of a vacuum in the distortional plan section. Notably, the effect of water entrainment phenomena on flow rate and velocity is diminished in the scale model test, emphasizing the advantage of numerical simulation in predicting hydraulic parameters for the prototype. On this basis, the optimization of the gate shaft arrangement is executed through numerical simulation; the results indicate that the vacuum issues in the contraction section were partially resolved through structure optimization. The simulation values are close to the experimental results, and the modified design of the tunnel can be used in a water conveyance project.