Catalyst particle shapes and pore structure engineering are crucial for alleviating internal diffusion limitations in the hydrodesulfurization (HDS)/hydrodenitrogenation (HDN) of gas oil. The effects of catalyst particle shapes (sphere, cylinder, trilobe, and tetralobe) and pore structures (pore diameter and porosity) on HDS/HDN performance at the particle scale are investigated via mathematical modeling. The relationship between particle shape and effectiveness factor is first established, and the specific surface areas of different catalyst particles show a positive correlation with the average HDS/HDN reaction rates. The catalyst particle shapes primarily alter the average HDS/HDN reaction rate to adjust the HDS/HDN effectiveness factor. An optimal average HDS/HDN reaction rate exists as the catalyst pore diameter and porosity increase, and this optimum value indicates a tradeoff between diffusion and reaction. In contrast to catalyst particle shapes, the catalyst pore diameter and the porosity of catalyst particles primarily alter the surface HDS/HDN reaction rate to adjust the HDS/HDN effectiveness factor. This study provides insights into the engineering of catalyst particle shapes and pore structures for improving HDS/HDN catalyst particle efficiency.