Objectives The intestinal flora is associated with the occurrence of MG, but the biological relevance of these associations is often unclear. We conducted a study to determine whether intestinal flora and metabolites are disturbed in individuals with MG, especially in patients not administered drugs. Methods In this study, stool samples were obtained from 50 individuals with MG, and 15 matched healthy controls (HCs). Then, 16S ribosomal RNA (rRNA) gene amplification sequencing (V3-V4 region) and gas chromatography-mass spectrometry were used to investigate the composition and structure of the intestinal flora community and the levels of metabolites in patients with MG and HCs. Clinical characteristics were collected, including MG quantitative scoring (QMGS), MG activities of daily living (MG-ADL) score, MG-specific quality-of-life 15 (MG-QOL-15) score, manual muscle testing (MMT) score, and acetylcholine receptor antibody titer levels. These parameters were used to analyze the correlation between distinct flora and clinical features. Results A prominent difference in the intestinal flora was found between the MG and HC groups. The MG intestinal flora is characterized by an increase in the enrichment of microorganisms such as Escherichia-Shigella, Fusobacterium, and Ruminococcus and a decrease in the enrichment of Lachnospira, an anti-inflammatory bacteria. Lachnospira showed a negative correlation with QMGS, MG-ADL score, MG-QOL-15 score, and acetylcholine receptor antibody titer, while demonstrating a positive correlation with MMT score. Conclusion The intestinal flora and its metabolites play irreplaceable roles in MG, especially in individuals who are not