MX-80 granular bentonite is expected to be used as a buffer material for high level nuclear waste storage in Switzerland. This material is composed of 85% of smectite clay and exhibits a particular structure with four different scales. MX-80 macroscopic properties can therefore be investigated using upscaling techniques, but this approach needs a comprehensive understanding of the material fabric. In the present work, intrinsic permeability of MX-80 has been derived from available data on the structure arrangement with three upscaling steps. The missing structural parameters (permeability of clay stacks, their shape and the shape of micropores) can be estimated and it is shown that the permeability derived using a self-consistent scheme is in good agreement with experimental measurements for reasonable values of these parameters. The influences of these parameters variations have been investigated. The ranges of values in which they play a key role on the permeability derivation for structures like the one of MX-80 have been highlighted.