Modern methods for the synthesis of nanocomposites do not allow simultaneous control of their chemical, morphological, and microstructural properties. By H. Khan, T. Reisinger and their colleagues [1] a new method was developed for creating fully adaptable nanocomposites by combining cluster ion beams and thin-film deposition technologies for the manufacture of cluster nanocomposites under well-defined conditions. These processes are very complex; therefore, the application of mathematical modeling methods to their analysis is highly relevant. In this work, on the basis of mathematical modeling in nanosystems [2], a technique has been developed for modeling the implantation of cluster ion beams into a metal substrate. The results of numerical calculations at different substrate temperatures and velocities of cluster ion beams are presented.