With increasing urbanization and climate change exacerbating urban flooding and pollution, deep tunnel systems are being constructed in major Chinese cities to alleviate these issues. This paper presents a design optimization study for the lining structure of deeply buried shield-driven water conveyance tunnels passing through complex geological conditions, focusing on the Western Channel Expansion Project of the Hangjiahu South Drainage System. A refined three-dimensional finite element method was employed to evaluate the stress and deformation characteristics of the tunnel lining across three distinct geological cross-sections: moderately weathered muddy siltstone, an upper-soft-lower-hard stratum, and a weak rounded gravel layer. Key findings reveal that operational and maintenance conditions yield similar bending moments, but operational axial forces are significantly lower due to internal water pressure effects. Extreme values occur predictably: maximum positive bending moment/minimum axial force near the crown (0°) and invert (180°), and maximum negative bending moment/maximum axial force near springlines (90°, 270°). Internal force redistribution occurs across segments due to joint presence. While b8 and b10 schemes meet requirements in m1/m2 strata, the b8 division demonstrates superior mechanical performance in the critical weak m3 stratum, exhibiting higher safety factors and lower convergence deformations. Furthermore, joint configuration optimization (J0-J4) for the b8 lining in the m3 stratum indicates that increasing longitudinal bolt spacing (J1) is the most effective and economical method, reducing maximum bolt tensile stress by 9.83% compared to the base design (J0), with marginal improvements in load-bearing safety. These findings provide valuable guidance for the design of lining structures in similar deeply buried shield tunnels under complex hydro-geological loads.