[Purposes] As an important project to facilitate smooth waterway traffic, navigation tunnels pose a threat to the safety of ship navigation due to their narrow spatial environment. This study investigates the impact of tunnel dimensions and the complex internal navigation environment on ship navigation, focusing on 1000t container ships under different tunnel scales to ensure safe passage for ships. [Methods] A three-dimensional numerical model of the KCS ship navigating through a tunnel is developed based on the Reynolds-averaged Navier–Stokes (RANS) equations and the k-ω turbulence model. The study systematically analyzes the propagation and evolution of ship-generated waves within the tunnel, proposes optimal tunnel dimensions and vessel motion parameters for safe navigation, and evaluates the wave attenuation effect of a net-cage-type wave dissipation structure. [Findings] The findings reveal that the height of the stern solitary wave increases with the ship’s draft and the navigable water depth but decreases with increasing tunnel width. The maximum water level drop induced by ship-generated waves decreases as vessel speed and tunnel width increase but increases with greater draft and navigable water depth. The optimal width-to-depth ratio for safe navigation is B/h=8.13, the optimal navigation depth ratio is hi/h=0.88~0.94, and the optimal speed is Fr≤1.0. Regarding wave dissipation performance, the net-cage wave dissipation structure effectively suppresses the generation of stern solitary waves, achieving a maximum reduction rate of 39.19% in the stern wave disturbance range and improving the maximum water level drop by up to 50.01%. [Conclusions] The study demonstrates that tunnel width, water depth, vessel speed, and draft have a coupled effect on the evolution of ship-generated waves. The net-cage structure effectively mitigates the disturbance of the tunnel's internal water body caused by vessel navigation, providing a theoretical basis for ensuring the safety and stability of ship passage through navigable tunnels.