In response to the limitations of traditional methods such as Kriging, which rely on reference planes and are difficult to handle spatially multi-valued overlapping geological structures, this paper proposes a multi-valued complex geological structure modeling method based on Discrete Smooth Interpolation (DSI). Through dimensionless constrained iterative calculation of topological grids, DSI dynamically approximates discrete sample points, effectively solving the problem of spatial multi-value correspondence and getting rid of the reliance on coordinate systems in traditional methods. This method is applicable to the modeling of complex structures such as caves, lens bodies, folds and reverse faults, and has been integrated into the GeoStation (Geological 3D Survey and Design System), significantly improving the accuracy of multi-value regional reconstruction and providing a new solution for complex geological modeling.