Hydrodesulfurization catalysts have two types of active sites for hydrogenation and hydrogenolysis reactions. While hydrogenation sites are more active for desulfurizing refractory sulfur species, they are more susceptible to organonitrogen inhibition than hydrogenolysis sites. In contrast, hydrogenolysis sites are more resistant to organonitrogen inhibition but are less active for desulfurizing refractory sulfur species. This dichotomy is exploited to develop an ultradeep hydrodesulfurization stacked-bed reactor comprising two catalysts of different characteristics. The performance of such a catalyst system can be superior or inferior to that of either catalyst alone. A mathematical model is constructed to predict the optimum stacking configuration for maximum synergies between the two catalysts. The best configuration provides the precise environment for the catalysts to reach their full potentials, resulting in the smallest reactor and minimum hydrogen consumption. Model predictions are consistent with experimental results. A selectivity-activity diagram is developed for guiding the development of stacked-bed catalyst systems. (c) 2017 American Institute of Chemical Engineers AIChE J, 64: 595-605, 2018