This study performed a representative elementary volume (REV) and 3D equivalent continuum study of rock fractures based on fluid simulations of 3D discrete fracture networks (DFNs). A series of 3D DFNs with heterogeneous aperture distributions (the DFN-H model) and uniform apertures (the DFN-I model) were established, in which the fractures were oriented according to the geological field mapping of a high-level radioactive waste candidate site in China. The 3D DFNs of the different model sizes were extracted and rotated in a number of directions to check whether there was a tensor quality of the permeability at a certain scale. The results show that aperture heterogeneity increases the REV size and results in a necessarily larger model size to reach an equivalent continuum behavior, and this effect is more obvious when the fracture density is smaller. The shape of the 2D permeability contour is irregular, with some breaks when the model size is small. As the model size increases, its shape gradually tends to become smooth and approaches an ellipse. The shape of the permeability contours of the DFN-H model is slender compared to the DFN-I model, indicating a larger difference between the minimum and maximum values of the permeability. For the DFN-H model, there is no appropriate approximation for the equivalent permeability tensor over the studied model size range, whereas a good fit of the permeability ellipsoid is obtained for the DFN-I model, and the 3D directional permeability is calculated at this model scale. The corresponding magnitude and direction of the principal permeability are obtained, which can be viewed as the equivalent permeability tensor for the approximated continuum medium.