The microstructure evolution of 4H-SiC under the implantation of hydron ions and copper ions was investigated using molecular dynamics (MD) simulations and experimental analysis. MD models were developed to simulate the implantation of single Cu2+ and H+ ions into SiC, analyzing lattice damage, amorphous defects, and temperature distribution. H+ ion implantation resulted in a higher number of amorphous atoms compared to Cu2+ ions. The maximum atomic temperature during Cu2+ ion implantation was significantly higher (1635 K) than during H+ ion implantation (950 K), although the volume of the temperature rise region was larger in the H+ model. Cu2+ ions induced more severe lattice vibrations than H+ ions. Atom movement along regions of weak lattice binding energy was observed. The study also examined overlapping multiple ion implantations, considering ion type, initial energy, and incident angle. Cu2+ ions exhibited smaller sputtering yield, projection range, number of amorphous atoms, and energy increment compared to H+ ions. A 0° incident angle resulted in higher sputtering yield and increased amorphous structure formation due to the channeling effect, which was more pronounced in the H+ model. The experimental results demonstrate that compared to Cu2+ ions, H+ ions have a greater impact on the surface peak roughness, sub-surface damage depth, and surface damage of SiC samples. It can provide a reliable guidance for selecting process parameters and the types of ions to implant.