According to the fractal scaling law of microstructures, the particle and pore structures of random porous media were reconstructed with Monte Carlo method. The seepage property of multiscale porous media was studied with a fractal capillary bundle model. A quantitative relation between macroscopic seepage properties and microscopic structures was addressed. It shows that microstructures of porous media reconstructed by the fractal Monte Carlo method are close to that of real media. Calculated results for gas flow through porous media agree well with those by lattice Boltzmann method. It is shown that gas permeability increases with the increment of Knudsen number. The pore fractal dimension takes important effect on the microscale effect of gas flow through porous media, while the influence of tortuosity fractal dimension on the ratio of apparent gas permeability to intrinsic permeability is marginal. The method shows advantages that the convergence speed is fast and the calculation error is independent of dimension. It is helpful in understanding seepage mechanisms of multiscale porous media.