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Potassium dihydrogen phosphate (KDP) is an important nonlinear material due to its excellent physical and optical properties. However, it is also a difficult-to-machine material due to its complex anisotropic microstructure. To better understand the deformation mechanisms under external stresses, this paper aims to carry out systematic nanoindentation simulations using molecular dynamics (MD). To facilitate the structural characterization of KDP, a machine learning-based method was developed. The results showed that the subsurface damage is obviously anisot