Assessing the long-term safety of geological repositories for high-level radioactive waste is critically dependent on understanding radionuclide transport in multi-scale fractured rocks. This study explores the influence of upscaled parameters on radionuclide movement within a three-dimensional fracture-matrix system using a discrete fracture-matrix (DFM) model. The developed numerical simulation workflow includes creating a random discrete fracture network, meshing of the fractures and matrix, assigning upscaled parameters, and conducting finite element simulations. We simulated the spatiotemporal evolution of radionuclide concentrations in the fractures and matrix over a century, revealing significant spatial heterogeneity driven by a heterogeneous seepage field. Employing geostatistics-based upscaling methods, we predicted the effective ranges of crucial solute transport parameters at the field scale. The matrix diffusion coefficient, matrix distribution coefficient, and longitudinal dispersivity were upscaled by factors of 2.0–3.0, 2.5–4.0, and 10–104, respectively, based on laboratory-scale measurements. Incorporating these upscaled parameters into the DFM model, we analyzed their impact on radionuclide transport. Our findings demonstrate that an upscaled matrix diffusion coefficient and matrix distribution coefficient result in a delayed transport of radionuclides in fractures by enhancing mass transfer between the fractures and rock matrix, while an upscaled longitudinal dispersivity accelerates transport by advancing the positions of concentration peaks. Sensitivity analysis revealed that the matrix distribution coefficient is the most impactful, followed by dispersivity and matrix diffusion coefficient. These insights are important for minimizing parameter uncertainties and enhancing the accuracy of predictions concerning radionuclide transport in multi-scale fractured rocks.