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Groundwater models are critical for simulating subsurface hydrological processes and guiding informed policymaking for groundwater management. However, the widely applied groundwater models typically use regularshaped grids to discretize aquifer systems and require that the directions of the grid edges are aligned with the hydraulic conductivity tensor. Such rigorous requirements for spatial discretization have constrained the models' application in aquifer systems with anisotropic hydrogeological characteristics. To address such limitations, we develop an improved groundwater flow model based on the multipoint flux approximation (MPFA) method in this study. The new model allows us to use arbitrary-shaped polygon grids to discretize aquifer systems and relaxes the rigorous requirement of the alliance between polygon edges and hydraulic conductivity tensor. The functionality and performance of the new model are demonstrated by comparing the output between our model, MODFLOW, and analytical solution in four case studies with various hydrogeological conditions. In a real-world watershed with complex-shaped boundaries, our model outperforms the conventional groundwater model in boundaries. The modeling results show that our model can yield accurate simulation of subsurface hydrological processes in aquifer systems with complex-shaped boundaries. Furthermore, our model can provide a more flexible discretization solution to couple surface water and groundwater model in integrated hydrological model development.