The role of Pediococcus pentosaceus in the gastrointestinne has received considerable attention in recent decades. This study aimed to investigate the effects of the short-term administration of P. pentosaceus on physiological characteristics, inflammation, and intestinal microecology in mice. In this study, 90 male C57BL/6J mice were divided into 15 groups, with 14 groups treated with a daily intragastric administration of different genotypes of P. pentosaceus. After three weeks of intragastric administration P. pentosaceus had a mild effect on mice. It could be seen that different P. pentosaceus strains had different effects on the gut microbiota and intestinal microecology. P. pentosaceus VCQYC5144M12 possessing an Enterolysin A operon may have been harmful, activating the expression of inflammatory factors, while P. pentosaceus DYNDL69M8 consisting of only a pediocin-like operon increased the abundance of beneficial bacteria and increased the content of acetic acid. The presence of various genotypes of bacteriocin may have been the explanation for variations among strains. This may provide theoretical support for further exploring the probiotic effect and patterns of P. pentosaceus.