Probabilistic safety assessment (PSA) of nuclear facilities on external multi-hazards has become a major issue after the Fukushima accident in 2011. However, the existing external hazard PSA methodology is for single hazard events and cannot cover the impact of multi-hazards. Therefore, this study proposes a methodology for quantifying multi-hazard risks for nuclear energy plants. Specifically, we developed an efficient multi-hazard PSA methodology based on the probability distribution-based Boolean algebraic approach and sampling-based method, which are currently single-hazard PSA methodologies. The limitations of the probability distribution-based Boolean algebraic approach not being able to handle partial dependencies between the components are solved through this sampling-based method. In addition, we devised an algorithm that was more efficient than the existing algorithm for improving the limits of the current sampling-based method, as it required a significant computational time. The proposed methodology was applied from simple examples to single-and multi-hazard PSA examples of actual nuclear power plants. The results showed that the proposed methodology was verified in terms of accuracy and efficiency perspectives. Regarding the sampling-based method, it was confirmed that the proposed algorithm yielded fragility and risk results that have similar degrees of accuracy, even though it extracted a smaller number of samples than the existing algorithm.