For the treatment of uncertainties arising in the safety assessment of high-level radioactive waste repository, a new probabilistic safety assessment methodology is developed. The present methodology describes a radioactive waste repository as a stand-by redundant system in a continuous operation using the system reliability analysis method in order to consider the model uncertainties. The risk of waste repository is presented as a product of the failure probability density of repository and the radionuclide inventory in the repository when the failure of respository occurs. Simultaneously, to evaluate how the safety assessment results are affected by the uncertainties involved in input parameters, the Monte Carlo simulation with Latin Hypercube sampling and a statistical estimation are used.