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Background Dietary essential oil (EO) supplementation can exert favorable effects on gut health in broilers. However, it is unknown whether EO could improve intestinal functions, consequently beneficial for egg performance and quality in late-phase laying hens. This study was aimed to investigate the potential effects of EO on production performance, egg quality, intestinal health and ileal microbiota of hens in the late phase of production. A total of 288 60-week-old Hy-line Brown laying hens were randomly divided into 4 groups and fed a basal diet (control) or basal diets supplemented with oregano EO at 100, 200 and 400 mg/kg (EO100, EO200 and EO400). Results Dietary EO supplementation resulted in a quadratic decrease (P < 0.05) in feed conversion ratio with lower (P < 0.05) feed conversion ratio in EO200 group than the control during weeks 9–12 and 1–12 of the trial. Compared to the control, EO addition resulted in higher (P < 0.05) eggshell thickness at the end of week. 4, 8 and 12 and higher (P < 0.05) chymotrypsin activity. There was a quadratic elevation (P < 0.05) in ileal chymotrypsin and lipase activity, along with a linear increase in villus height to crypt depth ratio. Quadratic declines (P < 0.05) in mRNA expression of IL-1β, TNF-α, IFN-γ and TLR-4, concurrent with a linear and quadratic increase (P < 0.05) in ZO-1 expression were identified in the ileum with EO addition. These favorable effects were maximized at medium dosage (200 mg/kg) of EO addition and intestinal microbial composition in the control and EO200 groups were assessed. Dietary EO addition increased (P < 0.05) the abundances of Burkholderiales, Actinobacteria, Bifidobacteriales, Enterococcaceae and Bacillaceae, whereas decreased Shigella abundance in the ileum. Conclusions Dietary EO addition could enhance digestive enzyme activity, improve gut morphology, epithelial barrier functions and modulate mucosal immune status by altering microbial composition, thus favoring feed efficiency and eggshell quality of late-phase laying hens.