Molecular dynamics simulation was used to investigate the diffusion behaviors of Zr and Si atoms during a reactive diffusion which produces Zr silicide. The simulation results were compared with those in Roy's experimental results. The profiles of mean square displacements (MSDs) of Zr and Si atoms at different temperatures were first used to evaluate the melting point above which the significant inter-diffusions of Zr and Si atom occur. The diffusion coefficients near the melting point were derived by the Einstein equation from MSD profiles. On the basis of diffusion coefficients at different temperatures, the diffusion barriers of Zr and Si atoms can be calculated by the Arrhenius equation. Compared to the corresponding experimental values, the predicted diffusion barriers at the Zr-Si interface were 23 times lower than the measured values in Roy's study. The main reason for this is that the Zr and Si atoms within the inter-diffusion region form different local ZrSi crystal alloys in the experiment, resulting in the lower diffusion coefficients and higher diffusion barriers found in the experimental observation.