In this work, a trickle-bed reactor coupled with catalyst pellet model is employed to understand the effects of the temperature and catalyst pellet structures on the reaction–diffusion behaviors in gas oil hydrodesulfurization (HDS). The non-isothermal reactor model is determined to be reasonable due to non-negligible temperature var-iation caused by the reaction heat. The reaction rate along the reactor is mainly dominated by the temperature, and the sulfur concentration gradient in the catalyst pellet decreases gradually along the reactor, leading to the increased intal effectiveness factor. For thefixed catalyst bed volume, there exists a compromise between the catalyst reaction rate and effectiveness factor. Under commonly studied catalyst pellet size of 0.8–3 mm and porosity of 0.4–0.8, an optimization of the temperature and catalyst pellet structures is carried out, and the optimized outlet sulfur content decreases to 7.6 wppm better than the commercial level at 0.96 mm of the catalyst pellet size and 0.40 of the catalyst porosity.