Isobutyl alcohol with good miscibility, high octane number and energy density has been paid more and more attention in the field of new biofuels, as it is an ideal alternative fuel for gasoline. However, isobutyl alcohol and water azeotrope need a clean and efficient separation method to realize the separation in isobutyl alcohol production process and industrial wastewater. Three hydrophobic deep eutectic solvents (DESs) were used to separate isobutyl alcohol. Decanoic acid was used as hydrogen bond donor and menthol, thymol and lidocaine were used as hydrogen bond acceptors to synthesize DESs. The liquid-liquid equilibrium experiment was carried out for the system containing DESs and MSD −water at 101.3 kPa and 303.15 K, and the separation effect of different DESs was indicated using distribution coefficient (β) and selectivity (S). The σ-Profile can be a good reflection of the strength of a substance's ability to accept and provide hydrogen bonds. The interaction energy and self-diffusion coefficient of the separation system were described quantitatively by molecular dynamics simulation. The relationship between DESs and the separation system was analyzed quantitatively by radial distribution function and spatial distribution function. The separation results show that the three DESs have good separation effect on isobutyl alcohol-water system, among which the DESs synthesized by thymol and decanoic acid has the best separation effect, and the interaction of isobutyl alcohol-water separation process is controlled by van der Waals forces. DESs plays an important role in the separation and treatment of isobutyl alcohol-containing wastewater, and promotes the sustainable development of wastewater treatment projects to save costs and increase production benefits.