Traditional longitudinal seismic analysis of subaqueous shield tunnels relies on uniform soil spring models which ignore the critical effects of abrupt soil stratum mutations on structural responses. This study proposes an improved Space Variant Generalized Response Displacement Method that incorporates space variant subgrade reaction moduli mapped directly from heterogeneous marine sites. Utilizing a refined shell spring model, the dynamic responses of a two point two kilometer full scale subaqueous shield tunnel are simulated under multi frequency beat waves and sea bed long period natural ground motions. Numerical results demonstrate that the spectral characteristics of ground motions significantly affect the features of the longitudinal non uniform dynamic responses of the tunnel. Under single frequency beat wave excitations, the traditional uniform soil spring model exhibits excessive seismic design redundancy within soft soil zones. Crucially, under broadband long period ground motions, the conventional approach triggers dual risks by significantly overestimating ring joint openings within soft soil sectors while severely underestimating both localized shear stress spikes at rock soil interfaces and joint openings within hard rock constrained segments. The proposed method effectively rectifies these deficiencies, achieving an optimal trade off by eliminating blind design margins in soft soils and precisely capturing hidden structural vulnerabilities induced by abrupt stratum mutations. This research provides a refined theoretical benchmark for targeted longitudinal seismic mitigation in super long underwater shield tunnels.