The kinetics of hydrodenitrogenation (HDN) were systematically studied in an isothermally high-throughput reactor over three kinds of catalysts (CoMo, NiMo, and NiMoW) to produce clean diesel meeting the latest national standard of China. The influences of reaction temperature, reaction pressure, volume ratio of H-2 to oil, and space time on hydrodenitrogenation were investigated to obtain kinetic parameters. Two kinetic models considering the influence of self-inhibition were proposed for the HDN reaction of diesel oil. The results of both models are satisfactory. Taking the two-lump model as an example, it could well predict the evolution of nitrogen-containing compounds' concentration along the axial length of the reactor, and the simulation on the HDN activity of various catalyst stacking schemes is close to the experimental data, which proves that the model is applicable for the simulation of a catalyst stacking system. In addition, the concentration of nitrogen-containing compounds was predicted for the catalyst gradation model of different loading sequences.