Abstract: The radiation damage has become a hot focus in materials and computer field. Molecular dynamics method (MD) and kinetic Monte Carlo method (KMC) are two commonly used methods to study the phenomenon. Due to the MD and KMC simulation system have different atom types, variables and data representations. It is an important issue to realize the data transmission between the two systems. Therefore, we develop a middle program to build a bridge between the two simulations, and puts forward shortest distance algorithm (SD) which can identify the type of atom in the system. The SD algorithm identifies the type of atom in the system by calculating the distance between the atomic location and the standard grid point. Finally, this paper verifies the correctness and effectiveness of the SD algorithm and coupling simulation between MD and KMC.