The rock strength in an active fault zone is low and the surrounding rock is fractured and has poor stability, making any subsea tunnel crossing the active fault zone extremely susceptible to disasters such as tunnel collapse, sudden water ingress, and mud inrush. This poses a potential threat to the construction project, making the dynamic stability analysis of a subsea tunnel crossing an active fault zone of great significance. This study takes the second subsea tunnel crossing the Cangkou Fault in Jiaozhou Bay as the engineering background and conducts numerical simulations by employing different lining stiffnesses for tunnel excavation, as well as applying dynamic loads. The dynamic stability of the subsea tunnel crossing the active fault zone is evaluated by comparing and analyzing the lining’s displacement, peak acceleration, and stress characteristics. This study explores the disaster-causing mechanisms of active fractures, determining that the hazard of orthogonal misalignment in an active fault zone is the least severe, while the hazard of opposite misalignment is the most severe. This research provides a basis for disaster prevention and mitigation in active fracture zones.