This study optimized the extraction process of essential oil from Tsaoko Fructus using deep eutectic solvents (DES) and explored its mechanism in promoting gastrointestinal peristalsis. DES composed of choline chloride and lactic acid (molar ratio 1∶2) was prepared, with optimal extraction parameters determined as water content 20%, solid-to-liquid ratio 1∶4 (g/mL), extraction temperature 70 ℃, extraction time 20 min, and distillation time 4 h, achieving an essential oil yield of 3.6%. Distillation time was identified as the critical factor (F=35, P<0.05). The Tsaoko Fructus essential oil administration group significantly reversed loperamide hydrochloride-induced gastrointestinal motility inhibition in rats in a dose-dependent manner. The abundance of Bacillota increased from 91.26% to 93.31% (P<0.01), while Verrucomicrobiota decreased from 4.45% to 1.37% (P<0.01). Metabolomics revealed that the essential oil regulated pathways such as primary bile acid biosynthesis, normalizing the distribution of differential metabolites. Microbiota-metabolite correlation analysis further indicated a positive association between Bacillota and bile acid metabolites (glycocholic acid, P<0.05), and a significant correlation between Verrucomicrobiota and inflammatory metabolites (7α-hydroxy-3-oxo-4-cholestenoate, P<0.001). This study provides valuable insights and references for the efficient and environmentally friendly extraction as well as the utilization and development of volatile oils from Tsaoko Fructus.