The purpose of this study is to develop the analysis procedures for the evaluation of the structural integrity of the spent fuel in normal condition of transport at sea. Spent nuclear fuel must be transported from the wet storage facility in the nuclear power plant to the intermediate storage facility, and the structural integrity must be maintained in vibration and shock loads during the transportation. In general, the transport of spent nuclear fuel is performed in three kinds of modes: road, rail, and sea. During transport, the spent nuclear fuel is subjected to repeated vibration and shock loads by road surfaces, railroad tracks, and waves of the sea. It should be evaluated whether the structural integrity of the spent fuel is maintained under these load conditions. All nuclear power plants in Korea are located in coastal sites, and the interim storage facility for spent nuclear fuel is highly likely to be decided as a coastal site as well. Therefore, the main mode of the spent nuclear fuel transport is expected to be maritime transport by ships. In this study, the analysis procedure was developed to evaluate the safety of spent fuel at maritime transport by ships, and the procedure for evaluating the integrity of spent fuel under normal conditions of maritime transport were proposed. CFD analysis using SeaFEM was performed for the vibration analysis of the ship by waves, and the structural vibration analysis of the transport system was simulated using the developed in-house codes. The fatigue durability of the cladding was also evaluated using the developed fatigue analysis program and the fatigue analysis used the strain data obtained from the structural analysis. It was concluded that the value of the fatigue damage on the spent fuel cladding during normal conditions of maritime transportation is close to “0” and the structural integrity of the spent fuel is maintained in the same condition.