The evolution of the continuous-atomistic approach to the simulation of processes of the interaction between high-energy heavy ions and metals is presented in this paper. The continuous-atomistic model is described by two different classes of equations, namely, thermal-conductivity equations with a source in the thermal-spike model and equations of motion of material points irradiated with a beam in a model of molecular dynamics. A software package is developed for simulation within the framework of the continuous-atomistic model. The results of simulation of the processes of metal-target irradiation with high-energy heavy ions depending on the parameters of the source function and the electron–phonon interaction coefficient are obtained.