In the face of increasingly serious environmental pollution problems, cleaner treatment of fuel products is of great practical significance. In the present work, a deep eutectic solvent capable of efficiently removing indole from simulated oils was prepared with a tetrabutylammonium bromide and acetic acid molar ratio of 1:2, and the extraction of indole was 98.88% with a distribution coefficient of 88.61 at an initial concentration of indole of 500 mg/L. The extraction mechanism was investigated by using FT-IR spectroscopy, which revealed that [TBAB:2AA] removes indoles by hydrogen bonding interactions with them. The density, viscosity, refractive index, and surface tension of the mixtures formed by [TBAB:2AA] with water over the full range of compositions were next measured as a function of temperature and composition of the mixtures, and the interactions between the DESs and water were discussed through excess properties. The excess properties indicate the formation of hydrogen bonds between water molecules and DESs and the insertion of water molecules into the DES network. There is a correlation between the extraction performance and physical properties of aqueous solutions of DESs. This work combines theory and application and is expected to provide a useful reference for the selection study of nitrogen removal agents.