Navigable tunnels with small cross-sections can be difficult to navigate. To improve navigational and economic efficiency, and navigational safety, comprehensive multi-objective optimization models are established based on the cross-sectional dimensions, navigational safety, and navigational capacity. First, for above-water and underwater tunnel cross-sections, multi-objective optimization functions including the underwater cross-sectional coefficient, navigational water depth, and tunnel outline dimensions are constructed, which are restrained by ship speed and structural clearance, respectively. Subsequently, a block-cage wave dissipation structure is designed and evaluated through numerical simulations to optimize the hydrodynamic conditions in tunnels. Finally, a three-dimensional numerical model of a 2 000-t class ship is developed to calculate wave height and flow velocity under different cross-sectional conditions, determine safe navigation speed limits, and develop an empirical formula. The major results are as follows: (1) The proposed optimization method effectively predicts underwater and above-water tunnel cross-sectional dimensions under navigational constraints. (2) The wave dissipation structure reduces the wave height and flow velocity by 30.69% and 51.34%, respectively, effectively improving hydrodynamic conditions. (3) The recommended safe navigation speed is 1.41－2.19 m/s for a 2000-t class ship in underwater tunnels with widths of 15.20－25.20 m. The empirical formula is applicable to various cross-sectional dimensions.