Underground structures can be vulnerable during strong earthquakes, and seismic mitigation systems designed for these structures are instrumental in improving multiple aspects of seismic performance. To deal with this problem, a novel isolation system is proposed for underground structures, employing the incorporation of a negative-stiffness amplification system (NSAS) and an isolator. The proposed NSAS consists of the subconfiguration of a spring with positive stiffness in parallel with a dashpot, which is then in series with a negative-stiffness device. The mechanical model and physical realization of the NSAS are presented, based on which the energy-dissipation-enhancement mechanism of NSAS is detailed. On this basis, comprehensive parameter analyses were conducted between the NSAS isolation system and a conventional isolation system. Analysis results showed that the NSAS exhibited a significant energy-dissipation-enhancement effect, in which the series connection of the negative and positive stiffnesses amplified the dashpot’s deformation for enhanced energy-dissipation capacity and efficiency. Compared with a conventional isolator, the NSAS isolation system provided the underground structure with a multiperformance and multilevel mitigation effect, particularly yielding lower responses of displacement and shear forces at the same time. More vibration energy could be dissipated by NSAS, thereby alleviating the energy-dissipation burden of underground structures.