Flooding in underground spaces, such as subway stations, underground malls, and garages, has increased due to intensified rainfall, urbanization, and population growth. Traditional 2D simulations often overlook crucial vertical flow variations, especially in steep transitions like stairs and ramps. The current study aims to investigate the flood dynamics in large underground geometries by taking a parking lot in Beijing, China, as a study case. The model overcomes the limitations of previous simulations by adapting a full 3D mesh-based simulation with reasonable computational cost. Unlike earlier studies, this model employs a high temporal resolution transient inflow at the inlet to the underground space. Simulation scenarios consider different return periods (5, 20, and 100 years) and inlet water depths, providing an analysis of their impact on flood status in the underground structure. The model generates high spatial–temporal results, enabling precise detection of flood-prone locations, evacuation times, and suggested mitigation techniques. The results recommend evacuating from hazard areas before the 10th minute during extreme flood events. Additionally, the study estimates a 40% increase in flood hazards for scenarios with direct connections between levels. Overall, the study highlights the importance of 3D simulations for accurate risk assessment.