Carbon cluster ion implantation is an important technique in fabricating functional devices at micro/nanoscale. In this work, a numerical model is constructed for implantation and implemented with a cuttingedge molecular dynamics method. A series of simulations with varying incident energies and incident angles is performed for incidence on silicon substrate and correlated effects are compared in detail. Meanwhile, the behavior of the cluster during implantation is also examined under elevated temperatures. By mapping the nanoscopic morphology with variable parameters, numerical formalism is proposed to explain the different impacts on phrase transition and surface pattern formation. Particularly, implantation efficiency(IE) is computed and further used to evaluate the performance of the overall process. The calculated results could be properly adopted as the theoretical basis for designing nano-structures and adjusting devices’ properties. Carbon cluster ion implantation is an important technique in fabricating functional devices at micro / nanoscale. In this work, a numerical model is constructed for implantation and implemented with a cuttingedge molecular dynamics method. A series of simulations with varying incident energies and incident angles is performed for the incidence on silicon substrate and correlated effects are more in detail. Meanwhile, the behavior of the cluster during implantation is also examined under elevated temperatures. By mapping the nanoscopic morphology with variable parameters, numerical formalism is proposed to explain the different impacts on phrase transition Particularly, implantation efficiency (IE) is computed and further used to evaluate the performance of the overall process. The calculated results could be properly adopted as the theoretical basis for designing nano-structures and adjusting devices’ properties.