Silicon carbide (SiC) is a promising semiconductor material for making high-performance power electronics with higher withstand voltage and lower loss. The development of cost-effective machining technology for fabricating SiC wafers requires a complete understanding of the deformation and removal mechanism. In this study, molecular dynamics (MD) simulations were carried out to investigate the origins of the differences in elastic–plastic deformation characteristics of the SiC polytypes, including 3C-SiC, 4H-SiC and 6H-SiC, during nanoindentation. The atomic structures, pair correlation function and dislocation distribution during nanoindentation were extracted and analyzed. The main factors that cause elastic–plastic deformation have been revealed. The simulation results show that the deformation mechanisms of SiC polytypes are all dominated by amorphous phase transformation and dislocation behaviors. Most of the amorphous atoms recovered after completed unload. Dislocation analysis shows that the dislocations of 3C-SiC are mainly perfect dislocations during loading, while the perfect dislocations in 4H-SiC and 6H-SiC are relatively few. In addition, 4H-SiC also formed two types of stacking faults.