Abstract: Although tunnel structures are confined by the surrounding strata, and relative movement between the structure and strata is not obvious under seismic loads, resulting in significantly superior seismic performance compared to surface structures, they are not entirely “seismic-free”. With the continuous development of the construction of tunnels and underground engineering, it is a major challenge for structural earthquake-resistant fortification design. Therefore, it is of great significance to conduct in-depth research on the seismic performance of underground structures and to promote their seismic resilience. First of all, the established tunnel seismic damage databases worldwide are reviewed. Based on the typical tunnel seismic cases, the main seismic damage characteristics are summarized, and the damage influencing factors and mechanisms are analyzed, respectively. Then, to effectively recognize the ground motion features of a rock mass, an extensive literature review is performed to explore the rate-dependent effect and the mechanical behavior under cyclic loading and unloading of rock and joint, and stress wave propagation principles in jointed rock. Additionally, from the perspective of seismic analysis of underground engineering structures, research progress and urgent key issues to be solved in the physical similarity experiment, dynamic time-history analysis, simplified seismic analysis method, wave analysis method, and seismic vulnerability analysis. Finally, the current common seismic protection countermeasures of underground structures are sorted out to provide a reference for seismic reinforcement of tunnels and underground projects in the future. It can be seen that tunnel lining will emerge with different degrees of damage during a certain level of earthquakes, such as slight cracks, spalling, leakage, dislocation, and collapse, which are related to ground motion parameters, structural characteristics, and geological conditions. Engineering rock mass exhibits a very strong rate-dependent effect. When it is subject to cyclic loading and unloading, the stress-strain curve will exhibit closed plastic hysteresis loops, and irreversible cumulative damage occurs. It is worthy of attention to develop a dynamic constitutive model that can characterize the rate effect and cyclic load properties of geotechnical and concrete materials and embed it into numerical simulation. Poor surrounding rock conditions will aggravate the acceleration, dynamic earth pressure, and strain response of the lining structure. Considering that the dynamic response of the lining structure crossing the fault zone is more intense, the study of structural response under coupling strong earthquake, fault dislocation, and high ground stress may be necessary. Since the sudden change of stiffness and the effect of stress concentration, the structural junctions and spatially overlapping sections between tunnel groups are often the weak links of tunnel seismic resistance. The simplified seismic analysis method considering the group cavities effect needs to be further explored. Integrating seismic vulnerability and functional recovery capacity of underground structures is a critical approach to enhancing seismic resilience. The combination of multiple protection strategies, the introduction of new materials, and new structural systems is the focus of future seismic protection design.