The objective of this study was to investigate the supplemental effects of the combination of benzoic acid and essential oils (BE) in nursery pigs. In Exp. 1, there were 5 dietary treatments including the negative control (NC), and the NC supplemented with BE at 1, 2, and 3 g/kg of feed and with benzoic acid at 5 g/kg [positive control (PC)]. Four levels of BE (0, 1, 2, and 3 g/kg feed) and 2 levels of BE (0 and 2 g/kg feed) were assayed in Exp. 2 and 3, respectively. One hundred and twenty Large White × Landrace barrows and 192 PIC L1050 × L337 barrows and gilts were used in Exp. 1 and 2, respectively. In Exp. 3, 24 PIC L1050 × L337 barrows and gilts were used. In Exp. 1, the supplemental BE increased average body weight of the pigs on day 14 of the trial, average daily gain (ADG) and average daily feed intake (ADFI) of days 1–14, and ADFI of days 1–28 quadratically (P < 0.050) while the gain: feed of days 1–14 was improved both linearly and quadratically (P < 0.050). In Exp. 2, the average body weight of pigs on day 14 of the trial, and ADG and ADFI of days 1–14 improved quadratically (P < 0.050) with the increasing supplementation of BE. In Exp. 3, The supplementation of 2 g/kg BE tended to decrease the relative abundance of the phylum of Bacteroides (P = 0.051) and the genera of Prevotellaceae Prevotella (P = 0.062). The principle coordinate analysis could differentiate the microbial community of the treatment supplemented with BE from the control group (P = 0.022). The analysis of the functional pathways of colonic microbiota showed that the supplemental BE upregulated caprolactam degradation, limonene and pinene degradation, and C5-branched dibasic acid metabolism, while downregulated the pathway of prostate cancer and the nucleotide-binding oligomerization-like receptor signaling pathway. In conclusion, BE improved the growth rate and feed intake in nursery pigs; the mechanism could be more due to the modulatory effect of BE on microbiota, and less related to the digestibility of energy and nutrients.