In the process of long-distance water conveyance tunnel construction, the unfavorable factors affecting the project safety often occur, such as defective strata. The underlying low-pressure layout method is an excellent approach addressing such problems. Taking a long-distance underlying low-pressure water conveyance project as the research object, a few sections, such as the box culvert, water diversion outlet, inlet and outlet shaft of the underlying low-pressure tunnel, underlying low-pressure tunnel section and some open flow tunnel sections were selected for the establishment of a three-dimensional numerical model. The RNG k-ε two-equation turbulence model combined with the VOF method was used to carry out the numerical simulation, and the distribution and change law of hydraulic characteristics along the underlying low-pressure long-distance water conveyance tunnel were studied for the comparison and selection of different tunnel schemes. According to the research, under different working conditions, the flow connection of each part of the underlying low-pressure tunnel was relatively smooth, and the phenomenon of alternating open and full flow did not occur. The velocity distribution in the inlet and outlet shaft of the underlying low-pressure tunnel was rather complicated. With the increase of the diameter of the inlet shaft, the distribution of water, gas and water surface line in the tunnel did not change much, the velocity gradient in the inlet shaft decreased, and the velocity distribution in the outlet shaft changed little. The research results can provide some reference for the design scheme of underlying low-pressure long-distance water conveyance tunnels.