Leakage defects at gasketed joints primarily induced by joint deformation and gasket ageing pose a significant challenge to the long-term safety of shield tunnels, leading to ground consolidation and structural deterioration of tunnel lining. A novel FEM analysis method was proposed to model the hydro-mechanical coupled behaviour of the joint during the long term, comprehensively incorporating a waterproof capacity degradation model, localised leakage behaviour characterised by cubic law, and correlations between joint deformation and gasket compression. The model was then validated by a full-scale experiment on the structural behaviour and the image tunnel method on the seepage field. The influence of localised leakage on soil-tunnel interaction and the structural responses of lining over the entire service duration was assessed, considering the effects of joint deformation, double-pair gaskets, number of leakage joints, and internal water pressure. The proposed method captures the initial waterproof stage of 40 years, followed by waterproof failure and progressive hydraulic deterioration of the joint. The localised leakage leads to increases in the bending moment, long-term settlement and ovalisation deformation. The use of double-pair gaskets effectively improves the waterproof capacity of the joint, extending the waterproof stages and mitigating further hydraulic deterioration. Additionally, the leakage pattern changes with the adoption of double-pair gaskets. The influence of internal water pressure is twofold: it enlarges the joint eccentricity and opening, exacerbating the waterproof capacity degradation; however, it also counteracts groundwater infiltration by reducing the hydraulic gradient. Internal water pressure primarily reduces axial forces, while leakage is mainly responsible for changes in bending moments and lining deformation.