This study numerically analyzed the effect of multiscale heterogeneity on flow and transport response of a threedimensional (3D) fractured porous rock with rough-walled fracture network. 3D discrete fracture matrix (DFM) models with different heterogeneity scales (network-scale, fracture-to-fracture-scale, and individual fracture scale) were generated. The results showed that the velocity and concentration distributions among the different DFMs were highly variable due to multiscale heterogeneity. The cumulative distribution function curves (CDFs) of the concentration disctribution indicated that fracture-to-fracture-scale heterogeneity led to an earlier breakthrough time than network-scale heterogeneity, and this behavior was further enhanced by individual fracture-scale heterogeneity, suggesting that transport was accelerated by enhanced local channeling flow with increasing fracture roughness. The complementary cumulative distribution function curves (CCDFs) showed obvious long tailing as heterogeneity increased from fracture-to-fracture-scale to individual fracture-scale. Compared with the case where only network-scale heterogeneity was considered, the calculated downstream concentration with fracture-to-fracture-scale heterogeneity increased first from 0.670 to 0.709. However, the downstream concentration then decreased from 0.684 to 0.618 as the roughness increased from & USigma; = 0.03 mm to & USigma; = 0.07 mm. These results can help predict the migration behavior of radioactive nuclides in far-field areas and assess the long-term performance of deep geological repositories.