In terms of safety operations, the cooling system is an essential component to remove decay heat in Spent Nuclear Fuel Storage Pool. The popular design for this cooling system consists of two heat exchangers (HE) where the pool water is cooled by cold water that has been chilled by a chiller. This investigation is done to discover the actual thermal efficiency of two HE at several variations of valve openings and the ability of cooling system in removing decay heat. The experiments conducted in the spent fuel storage pool that stored 287 elements of G.A. Siwabessy Multipurpose Reactor (GAS-MPR) spent nuclear fuel inventories. The variation of the cooling system opening valve were 12.5%, 25%, 50%, and 75%. The investigation results show that the larger opening valve improves thermal efficiency in both the primary and secondary HE. For the primary HE, in each variation of the valve openings, the average thermal efficiencies were obtained as 0.06, 0.15, 0.24, and 0.40, respectively. For the secondary HE, the average thermal efficiencies were obtained as 0.53, 0.62, 0.64, and 0.71, respectively. A significant increase in thermal efficiency occurs in the primary HE. This increased value, however, is still smaller than the secondary HE. From the measurement of pool water temperature under various conditions during ventilation operation, it is concluded that at various valve openings, the Spent Nuclear Fuel Storage Pool is still able to remove decay heat and maintain the pool water temperature below 26°C.