The complex structure represents a critical form for enhancing urban underground space utilization, characterized by its distinctive composite structural configuration and high-performance functional resilience requirements. There is a pressing need to advance research on seismic performance evaluation and resilience enhancement technologies. The inerter system, leveraging inertial amplification and tuning-based vibration absorption mechanisms, offers the ability to flexibly adjust inertial characteristics and control the dynamic response of the host structure. This paper proposes an inerter-based isolation system tailored for complex structures and delineates its installation methods, simulation methodologies, and parameter design procedures. Using a typical complex structure as an engineering case study, a numerical simulation analysis was conducted on the soil-inerter isolation system-complex interaction system and recommended design parameters for the inerter-based isolation system are provided. The results indicate that the design procedure of the inerter-based isolation system effectively correlates design parameters with the structural response of the complex, thereby achieving the seismic design objectives. The proposed system effectively controls acceleration, displacement, and stress responses of the complex structure. In comparison with conventional isolation schemes, it simultaneously satisfies the multi-objective coordinated control requirements of both the complex structure and the isolation layer. Moreover, while significantly mitigating the seismic response of the superstructure above the complex, the inerter-based isolation system does not adversely affect the seismic performance of the underground portion.