The images of granular ore media were captured by X-ray CT scanner. Combined with digital image processing and finite element techniques, the three-dimensional geometrical model, which represents the realistic pore structure of the media, was constructed. With this model, three dimensional pore scale fluid flow among particles was simulated. Then the distributions of fluid flow velocity and pressure were analyzed and the hydraulic conductivity was calculated. The simulation results indicate the fluid flow behaviors are mainly dominated by the volume and topological structure of pore space. There exist obvious preferential flow and leaching blind zones simultaneously in the medium. The highest velocities generally occur in those narrow pores with high pressure drops. The hydraulic conductivity obtained by simulation is the same order of magnitude as the laboratory test result, which denotes the validity of the model. The pore-scale and macro-scale are combined and the established geometrical model can be used for the simulations of other phenomena during heap leaching process.