Abstract: This study systematically investigates the design and seismic performance of ultra-deep underground water pool structures under complex geological conditions. Taking a 42-meter-deep underground submerged pool as example, the research focuses on the reinforced concrete pool structure and the foundation pit support system composed of secant piles combined with internal bracing, exploring its mechanical characteristics and seismic response in a miscellaneous fill–limestone composite stratum. The study first employs a three-dimensional finite element method for geotechnical modelling to simulate the entire process of foundation pit excavation, evaluating the deformation control and stability of the support structure. It investigates the computational assumptions, analytical methods, and shape optimization of the irregularly shaped pool structure under extreme hydrostatic pressure, completing crack resistance verification and anti-floating stability analysis under static conditions. Specifically, addressing the dynamic response under the coupled effects of seismic activity and high water pressure, elastoplastic time-history analysis is conducted using LS-DYNA software to quantify seismic hydrodynamic pressure and structural dynamic behaviour, with results compared and validated against traditional response displacement method calculations. The findings indicate that under static conditions, the crack width of the pool structure meet code requirements, and the anti-floating safety factor complies with design standards. Under seismic conditions, the reinforcement of the underground structure requires further enhancement compared to static conditions, with stress concentration observed at the interface between bedrock and soil layers. The displacement response of rectangular pool sections increases under rare earthquakes, and elastoplastic time-history analysis effectively identifies stress concentration areas, providing a basis for local structural strengthening. This study develops a comprehensive design methodology for ultra-deep underground pool structures under combined dynamic water level and seismic actions, covering the entire process from foundation pit support, static analysis, to dynamic seismic verification, offering design references and case studies for similar underground pool projects in complex geological environments.