To ensure the safe and reasonable development of karst caves, it is often necessary to consider the flood situation in the caves. Based on this, a method for determining the safe water level of karst caves based on three-dimensional (3D) geospatial information and flood numerical simulation is proposed. First, the Green-Ampt, soil conservation service unit hydrograph, and dynamic wave methods were used to build a mountain torrent model and verify its reliability. Second, flood hydrograph at the entrance of the karst was calculated using the designed 10-year rainstorm input flood model, and the flood data served as the input parameter for the flood simulation in the cave. Finally, a more efficient 3D turbulence model was selected to simulate the flood in the 3D model of the karst cave, then the safe water-level coordinates of the karst were extracted. Results show that the simulated flood mark is consistent with the observed flood mark. Therefore, the mountain flood model is suitable for flood calculation in the study area, and the 3D simulation results of the flood in the tunnel, based on large eddy simulation, are consistent with the actual water-level change characteristics in the tunnel. Thus, this method can provide more valid reference data on safe water levels for karst cave development.