In this work, a single particle model and particle-resolved reactor model are established at particle and reactor scales for HDN process of gas oil. In the aspects of optimal particle shape and size selection, the specific surface area of particle plays a decisive role at particle scale, while the interaction between reaction and diffusion resulting from the bed bulk density and total particle surface area is more crucial at reactor scale. In terms of selecting the optimal pore structure, the optimal pore diameter and porosity are found to be nonlinear correlated with particle specific surface area at particle and reactor scales, and the deviation is within an acceptable range. The optimal pore structures of HDN catalyst with given particle shape and size could be derived from the obtained correlation in the single particle model instead of the particle-resolved reactor model to greatly reduce the computational resources and time consumption.