A multi-scale scheme for the invasion percolation of rock fracture networks with heterogeneous fracture aperture fields is proposed. Inside fractures, fluid transport is calculated on the finest scale and found to be localized in channels as a consequence of the aperture field. The channel network is characterized and reduced to a vectorized artificial channel network (ACN). Different realizations of ACNs are used to systematically calculate efficient apertures for fluid transport inside differently sized fractures as well as fracture intersection and entry properties. Typical situations in fracture networks are parameterized by fracture inclination, flow path length along the fracture and intersection lengths in the entrance and outlet zones of fractures. Using these scaling relations obtained from the finer scales, we simulate the invasion process of immiscible fluids into saturated discrete fracture networks, which were studied in previous works.