A 3-D bond pore network model is presented and used to evaluate the effect of pore size and connectivity on the effective diffusion coefficient in random porous media. The control equations of the system are set up and the simulation method is discussed. The simulation results show that when the average pore size dm < 1 μm, the effective diffusion coefficient is strongly dependent on pore size. The analysis shows that Knudsen and bulk diffusion effects can be decoupled, and for any given diffusion conditions, the effect coefficient accounting for Knudsen diffusion can be obtained. Thus, the effect of pore size can been readily accounted for by correcting the bulk effective diffusivity with the Knudsen effect coefficient. The simulations also show that the percolation threshold in random porous materials decreases with increased pore network connectivity.