As a common zoonotic pathogen, Salmonella Typhimurium (S. Typhimurium) impairs the growth performance of broilers and also poses a threat to public health through the food chain. Probiotics as a kind of green microecological agents have been widely used to improve intestinal health. This study investigated the protective effect of combined use of Lactobacillus reuteri (L. reuteri) and Candida rugosa (C. rugosa) on reducing S. Typhimurium infection in broilers. A total of 144 one-day-old Arbor Acres (AA) broilers were randomly assigned to four groups: control (Con) group fed with a basal diet, Salmonella (Sal) group injected intraperitoneally with S. Typhimurium, antibiotic treatment (Sal+Ant) group, and probiotics supplementation (Sal+Pb) group. Combined probiotics were supplemented via drinking water from hatching throughout the experiment. S. Typhimurium was challenged at d 15, and samples were collected at 4 days later. Results showed that as antibiotic treatment, probiotics supplementation significantly improved body weight (BW), feed conversion ratio (FCR), and organ edema of broilers compared to Sal group (P < 0.05). Histological analysis of the ileum revealed that broilers in Sal+Pb group had higher villus height (VH) and crypt depth (CD), but lower histopathological score compared to Sal group (P < 0.05). Feeding probiotics compound also ameliorated the decrease of both mucus thickness and the number of goblet cells (GCs) induced by S. Typhimurium infection, consistent with the upregulation of MUC2 gene expression (P < 0.05) in the ileal mucosa. Furthermore, the colonization of Salmonella was also decreased in Sal+Pb group, accompanied with downregulation of pro-inflammatory cytokines genes expression (e.g., TNF-α, IL-1β) and upregulation of anti-inflammatory cytokine genes expression (e.g., IL-10) (P < 0.05) in the ileum. 16S rRNA sequencing showed that probiotics supplementation mitigated the Salmonella-induced decline in Bacteroides abundance, which exhibited positive correlations with cecal expression of anti-inflammatory cytokines (TGF-β, IL-10) and barrier-related genes (MUC2, ZO-1, ZO-2, Occludin) (P < 0.05). However, the increased abundances of Campylobacter and Escherichia-Shigella in the Sal group showed positive correlations with the relative weight of liver, heart and spleen to BW, but had negative correlations with BW and cecal expression of IL-10, MUC2, ZO-1, Occludin. (P < 0.05). These results indicate that combined use of L. reuteri and C. rugosa can greatly alleviate the gut injury induced by Salmonella infection through increasing mucin production, inhibiting pro-inflammatory cytokines and remodeling gut microbiota composition, and finally improve growth performance of broilers.