A 3D Kinetic Monte Carlo (KMC) model has been used to study the hydrogen isotope exchange from porous graphite at a single granule length scale (micrometers).The present KMC model is part of a previously reported multi-scale model developed by the authors [1]. SDTrimSP [2,3] simulations have been carried out and the results have been used to get some of the input parameters for the KMC where the diffusive-reactive aspect of H and D are studied. These SDTrimSP calculations show that the incident energetic ion beams lead to the development of inter-connected pores in the graphite sample. In the presence of these connected pores hydrogen molecule formation is not a local process. It takes place throughout the implantation zone and not only at the end of the ion range. For samples having less internal porosity mixing is very low. Therefore the internal structure of graphite, which affects the diffusion coefficient [4][5][6][7] and consequently molecule formation and atomic re-emission [8,9], plays the most crucial role for the H,D mixing. A new mechanism based on the KMC and SDTrimSP simulation is proposed to explain the experimental data.