Background:Salmonella pullorum is one of the most harmful pathogens to avian species. Magnolol and honokiol, natural compounds extracted from Magnolia officinalis, exerts anti-inflammatory, anti-oxidant and antibacterial activities. This study was conducted to evaluate the effects of dietary supplemental magnolol and honokiol in broilers infected with S. pullorum. A total of 360 one-day-old broilers were selected and randomly divided into four groups with six replicates:the negative control group (CTL), S. pullorum-infected group (SP), and the S. pullorum-infected group supplemented with 300 mg/kg honokiol (SPH) or magnolol (SPM). Results:The results showed that challenging with S. pullorum impaired growth performance in broilers, as indicated by the observed decreases in body weight (P<0.05) and average daily gains (P<0.05), along with increased spleen (P<0.01) and bursa of Fabricus weights (P<0.05), serum globulin contents, and the decreased intestine villus height and villus/crypt ratios (P<0.05). Notably, supplemental magnolol and honokiol attenuated these adverse changes, and the effects of magnolol were better than those of honokiol. Therefore, we performed RNA-Seq in ileum tissues and 16S rRNA gene sequencing of ileum bacteria. Our analysis revealed that magnolol increased theα-diversity (observed species, Chao1, ACE, and PD whole tree) andβ-diversity of the ileum bacteria (P<0.05). In addition, magnolol supplementation increased the abundance of Lactobacillus (P<0.01) and decreased unidentified Cyanobacteria (P<0.05) both at d 14 and d 21. Further study confirmed that differentially expressed genes induced by magnolol and honokiol supplementation enriched in cytokine-cytokine receptor interactions, in the intestinal immune network for IgA production, and in the cell adhesion molecule pathways. Conclusions:Supplemental magnolol and honokiol alleviated S. pullorum-induced impairments in growth performance, and the effect of magnolol was better than that of honokiol, which could be partially due to magnolol\'s ability to improve the intestinal microbial and mucosal barrier.