The production of ultralow-sulfur diesel from light cycle oil (LCO) by hydrotreatment is promising. Unfortunately, hydrodesulfurization (HDS) of LCO is seriously inhibited by the coexistence of organic nitrogen and aromatic compounds during the hydrotreating process. It is of great interest to understand this inhibition confidently by simulations. In this study, the inhibition effects from both organonitrogen and aromatic compounds are simulated by a proposed system dynamics (SD) model for the first time. The axial profiles of the concentrations of organic sulfur, nitrogen, and aromatics in the hydrotreating reactor are predicted by the SD model. Impact factors for nitrogen and aromatic compounds respectively are used to characterize their inhibition effects. Studies were also conducted on the variation of the impact factors along the axial position of the hydrotreator. The simulation results of HDS, with consideration of the nitrogen and aromatic inhibition effects, are compared with published experimental data. The influence of the operating conditions such as inlet system temperature and liquid hourly space velocity on the impact factors is also investigated.