Abstract: The junction of the subsea shield tunnel-shaft is prone to damage subjected to strong earthquakes. Taking the subsea shield tunnel crossing under the Shantou Gulf, China as a case study, the three-dimensional seismic response characteristics of the junction of the subsea shield tunnel-shaft are analyzed using the dynamic time-history analysis method (longitudinal axial + transverse + vertical shakings, longitudinal axil + vertical shakings) and the generalized response displacement method (longitudinal axial + transverse + vertical shakings), which considers the nonlinear dynamic behaviors of the seabed soil and concrete, the simulation of the bolt joints between ring segments by using multi-point constraints and connection elements as well as the ground motions produced by scaling from the strong earthquake records. The results show that under all the input bedrock motions with various characteristics, the deformation features between segment rings can be simulated effectively by the multi-point constraints and connection elements, and the opening widths between ring segments at the ring top and outside spandrel are larger. Serious seismic damage and stress concentration exist at the conjugate with direction of 45° of shaft. The seismic responses of the tunnel-shaft junction subjected to the earthquake motions with rich low frequency components are much stronger than those of earthquake motions with rich high ones. The seismic deformation and stress of the tunnel-shaft junction are much greater than those of the ring segments, and the influences of the horizontal shaking along the transverse direction of the tunnel on the seismic responses of the ring segments and the tunnel-shaft junction cannot be ignored. The spatial variation of the seismic responses of the ring segments along the tunnel longitudinal axis and the tunnel-shaft junction calculated by the two methods is consistent, whereas the seismic responses calculated by the generalized response displacement method are much larger than those calculated by the dynamic time-history analysis method.