The atomic-scale deformation behavior of the Silicon carbide (SiC) polytypes, including 3 C-SiC and 4 H-SiC, during the nanoindentation with different square-based pyramid indenter angles was investigated by molecular dynamics (MD) simulations. Detailed analyses were conducted on atomic displacement magnitude, atomic structure, radial distribution function and dislocation distribution were analyzed in-depth in both loading and unloading processes. The results show that the indentation deformation phenomenon of ‘‘pile-up’’ occurs with indenter angles below 120°. Maximum load shows a non-linear increase trend as the indenter angles increase. The residual depth of the 3 C polytype has insignificant fluctuations while that of the 4 H polytype generally increases as the angle decreases and fluctuates at the indenter angles of 100° ∼ 110°. The number of amorphous atoms in 4 H is greater than that of 3 C polytype. Most of the amorphous atoms recover to their original structure after the indenter is fully withdrawn. Dislocation analysis indicates that the total length of dislocation lines increases with larger indenter angles. The length of the 3 C dislocation line is greater than that of 4 H. At the same indenter angle, the dislocation slip depth of 3 C polytype is greater than that of 4 H polytype due to the different lattice stacking order of 3 C polytype is greater than that of 4 H polytype due to the different lattice stacking order.