This work evaluated the effects of natural deep eutectic solvent (NADES) treatments on the type and amount of Zanthoxylum bungeanum essential oil (EO). The yield of Z. bungeanum EO was improved from 4.67% in an untreated group to 6.42% in the Ch-LA (Choline chloride-Lactic acid) group. Significant difference in the relative content of main components from Z. bungeanum EO was observed among different NADES treatments, especially acid-based NADES treatments, which significantly raised the relative content of α-terpineol. Resultantly, the higher α-terpineol, the stronger the antimicrobial activity of Z. bungeanum EO. As one of the main components of Z. bungeanum EO, α-terpineol inhibited the growth of pathogenic bacterial strains by damaging the structure of cell membranes, disturbing cell physiological functions, and inducing DNA cleavage. In a word, selecting an ideal NADES treatment not only extracted the most EO but also improved the antibacterial activity.