The use of an aqueous solution of beta-cyclodextrin (beta-CD) as a molecular inclusion agent to simultaneously remove basic nitrogen (phenylamine and quinoline) and nonbasic nitrogen (indole) compounds, which are the main organic nitrogen compounds in light oil, is reported for the first time. The influence of various factors on the denitrification process, including the mass concentration of beta-CD, the denitrification time, the volume ratio of beta-CD aqueous solution to oil, the operation temperature, the presence of aromatic hydrocarbons and sulfides in light oil, and the regeneration performance were investigated, and the optimized denitrification conditions were obtained. Both the basic nitrogen and nonbasic nitrogen compounds were effectively removed by beta-CD aqueous solution, which is obviously superior to the current nonhydrodenitrification methods. Furthermore, the structures of the inclusion complexes of beta-CD with phenylamine, quinoline, and indole were studied by UV absorption, H-1 NMR, and Fourier transform infrared spectroscopy, X-ray diffraction, scanning electron microscopy, and computational simulations. A possible mechanism model for denitrification and the structures of the inclusion complexes are proposed on the basis of the analyses. This work lays the foundation for a novel denitrification method by molecular inclusion with beta-CD as a green bioresource material.