The machining of gallium nitride (GaN) wafers suffers from poor consistency due to the anisotropy of single crystal GaN, whose underlying mechanisms remain insufficiently studied. Herein, nanoindentation experiments and molecular dynamics (MD) simulation were performed on either Ga or N plane with one sharp edge of Berkovich indenter along \([2\overline{1 }\overline{1 }0]\) or \([01\overline{1 }0]\) to study the anisotropic deformation and fracture mechanisms of GaN. Compared to Ga plane, N plane demonstrates superior mechanical properties: higher hardness and elastic modulus, lower anisotropy, and better plastic deformability, supported by both MD simulations (e.g., earlier pop-in events, longer dislocation lines) and First-principles calculations (e.g., higher calculated elastic modulus). The consistent results from cathodoluminescence spectroscopy and MD simulations indicated that a greater number of slip bands and more severe surface damage emerged during one sharp edge of Berkovich indenter along \([2\overline{1 }\overline{1 }0]\) . Reasonable values of fracture toughness were calculated using different crack-length-based empirical formulas as well as the energy-based methods, demonstrating successful applications of indentation methods in characterizing fracture toughness of GaN. These results could be obtained by introducing a plastic deformation factor, modifying the formula based on fracture energy, and setting an appropriate critical void volume fraction (f* = 0.18). MD analysis shows that shear bands, slip bands, and atomic accumulation develop predominantly along \(\text{<}1{1}\overline{2 }0\text{>}\) directions due to the massive propagation of pure edge dislocations of the Burgers vector of 1/3 \(\text{<}1\overline{2 }10\text{>}\) . By elucidating the anisotropic mechanisms of GaN, this study provides a theoretical foundation for optimizing wafer precision machining, enhancing surface quality, and improving device reliability.