Employing catalytic decomposition to break down reducing agents in intermediate-level radioactive waste during nuclear fuel reprocessing offers significant advantages. This study focuses on investigating the deactivation behavior of 5% Ru/C catalysts by two different synthesis processes used for reducing agent destruction. Deactivation experiments were conducted by subjecting the 5% Ru/C catalysts to 100 and 150 reaction cycles. Changes in the concentration of free radicals on the carbon-based carrier were measured to analyze the loading position and loss of Ru ions. Additionally, sorption–desorption curves and pore size distributions of the four catalysts were obtained. Analysis results reveal that Ru ions on the catalyst adsorb onto active free radical sites on the carbon-based carrier. Under ultrasonic conditions, some Ru ions partially desorb from the free radical sites on the carbon-based carrier, and desorbed Ru ions may adsorb onto weak free radical sites, while undesorbed Ru ions may adsorb onto strong free radical sites. After hundreds of hours of reaction, SM1 and SM2 exhibited approximately a 30% decrease in specific surface area and pore volume compared to SM0. However, the catalyst activity remained unchanged, and the catalyst pore size remained essentially unchanged, which primarily means that the micropores on the catalyst’s surface have undergone corrosion and damage.