Ion implantation driven permeation (IDP) behavior on pure molybdenum has been investigated using deuterium ion with low energy (200–2000 eV). The experimental results include measurements of the dependence of the permeation rate at the steady state upon the incident ion flux, temperature and incident ion energy. A good linear relationship was observed between the permeation rate and the incident ion flux. This suggests that the IDP process through pure molybdenum was controlled by diffusion of deuterium in both the front and back regions. The temperature dependence of the permeation rate varies with the incident ion energy. It is caused by the different mechanism of diffusion of the hydrogen isotope in the front region due to the trapping effect for incident ion energy ranging from 1.5 to 2 keV, or the formation of a short diffusion path (H-SIA) for incident ion energy ranging from 200 to 500 eV.