With emphasis on safety, this study addresses for better design condition for the cooling system in a wet-type interim spent fuel storage facility, using a probabilistic safety assessment method. To incorporate the design renovation into the design phase, a simple approach is proposed. By taking the cooling system of a reference design, a fault tree analysis was performed to identify the weak point of the considered system, and then basic factors for design renovation were defined. A total of 21 design alternatives were selected through the combination of the basic factors. Finally, the optimum design alternative for the cooling system is derived by means of the cost and effect analysis based on the estimated cost, system reliability and assumed probabilistic safety criteria. With the assumption that the failure frequency of at-reactor spent fuel cooling system compiles with probabilistic safety criteria for the interim spent fuel cooling system, it was shown that the optimum alternative should have l00% cooling loop redundancy with one pump per cooling loop and a cleanup system installed separately from the main loop. Furthermore, it also should be classified into safety system. The result of this study can be used as a useful basis to identify factors of safety concern and to establish design requirements in the future. The method also can be applied for other nuclear facilities.