Parkinson's disease (PD) is characterized by the degeneration of dopaminergic neurons in the substantia nigra, and it has been reported that α-synuclein accumulates in the gut and then affects the brain along the gut-brain axis. In this study, we used Enterococcus faecium (EF), which was probiotics, that confer health benefits on the host when administered in adequate amounts. C57BL/6 mice, a model of PD induced by MPTP, were treated with EF (1ⅹ1012 CFU/mL). The study showed that motor dysfunction in MPTP-induced PD model mice improved. Additionally, EF was found to decrease the accumulation of overexpressed α-synuclein and increased the reduction of the tyrosine hydroxylase in the PD model. There were differences in microbiota composition and a relative abundance among the groups. The relative abundance of Bacteriodetes, Actinobacteria, and Proteobacteria was higher in the MPTP group than control group. However, the relative abundance of Firmicutes, and Verrucomicrobia all increased in EF groups, compared to MPTP. Moreover, levels of several inflammatory mediators, TNF-α, iNOS and COX-2, were overexpressed in PD. However, these mediators were reduced after EF treatment. Our analysis highlights that EF affects the gut microbiota and exerts a neuroprotective effect in the MPTP mice model. This study also provided insight into for microbially targeted therapy for PD.