Both hydraulic heterogeneity and topological one affect the tracer transport in real heterogeneous reservoir. Previous numerical studies for the fluid transport in 3D fractured medium focused on interpreting the topological heterogeneity, which were not able to analyze the combining effects by the local hydraulic heterogeneity of apertures. The authors developed a simple 3D discrete fracture set that had minimum geological heterogeneity but log-normal aperture distribution, and investigated the effect of hydraulic heterogeneity on the tracer transport using automatic quadrilateral meshing, finite element method, and streamline routing on irregular grids. Breakthrough curve assumed no retardation has a positively skewed characteristic, which confirms that the fluid transport is influenced by not only geological heterogeneity, but also pressure distribution and hydraulic diversity. A trajectory of streamlines and a distribution of residence time confirm that the tracer moves mainly in the direction of decreasing pressure gradient. The developed model can investigate the mixed effect of topological and hydraulic heterogeneity.