Abstract:[Background] With the carrying out of the antibiotics prohibition order, it is urgent to find a safe substitute for antibiotics. [Objective] The study aimed to explore the effects of the Pediococcus pentosaceus in finishing pigs. [Methods] 20 pigs were randomly divided into 2 groups with 2 replicates in each group and 5 pigs in each replicate. The pigs in control group were fed a basal diet, and the pigs in experimental group were fed with basal diet and Pediococcus pentosaceus (1010 CFU/kg), respectively. The experimental period was 28 days. [Results] The result data shows as follows: 1) There was no significant difference during two groups in the average daily gain (ADG), feed/gain(F/G) and average daily feed intake (ADFI) (P>0.05) during the experimental period. 2) It gained 1 036 OTUs by OTU cluster analysis, and they were clustered to 17 phyla, 23 classes, 37 orders, 67 families, 199 genus, 350 species. There was significant difference during two groups by principal co-ordinates analysis (PCoA) (P?0.05). At the phylum level, the relative abundance of Spirochaetes in group P was significantly higher than the group C (P?0.05). At the genus level, the relative abundance of Clostridium_sensu_stricto_1 and Terrisporobacter (P?0.05) in group P was higher than group C, Streptococcus (P?0.01), Lachnospiraceae_ XPB1014_group (P?0.05), Norank_f__p-251-o5(P?0.01) and Ruminococcaceae_NK4A214-group (P?0.05) was significantly lower than group C. The LEfSe (LDA effect size) results showed that 60 biomarkers were obtained when the LDA value was higher than 2.0, while 31 biomarkers were due to group P. The largest LDA value of bacteria in group P was Clostridiales, and that of group C was Streptococcus. 3) There was significant difference in positive and negative model by partial least squares discrimination analysis (PLS-DA) analysis (P?0.05), the two groups were divided completely. The metabolite analysis showed that the diphthamide, 2-hydroxymyristic acid, furanofukinin, dopaquinone, avocadene, N-(1-deoxy-1-fructosyl) proline and N-(1-deoxy-1-fructosyl) glycine up-regulated significantly (P?0.05) or extremely significantly (P?0.01) in group P, 24-dehydropro vitamin D3, Artonin U and 1alpha, 25-dihydroxy-9,11-didehydro-3-deoxy-vitamin D3, all down-regulated significantly (P?0.05) or extremely significantly (P?0.01). [Conclusion] In summary, the addition of pediococcus pentosaceus can optimize the structure of fecal microbiota in finishing pigs, improve the relative abundance of Clostridium_sensu_ stricto_1 and Terrisporobacter which due to disease-resistant, reduce the relative abundance of Streptococcus which is the opportunistic pathogen, improve the relative content of flavoring substance precursor (N-(1-Deoxy-1-fructosyl) proline, N-(1-deoxy-1-fructosyl) glycine), reduce the relative content of Vitamin D3 (24-dehydropro vitamin D3 and 1alpha,25- dihydroxy-9,11-didehydro-3-deoxy-vitamin D3). It has the potential function of growth-promoting and reducing disease.