There is a symbiotic relationship between gut microbiota and human beings. Imbalance of the gut microbiota will cause pathological damages to humans. Although many risk factors are associated with missed abortion (MA), the pathological mechanism of it is still unclear. Here, we analyzed gut flora of the patients with MA by S16 high-throughput sequencing. The possible pathogenic mechanisms of the MA were explored. Fecal samples from 14 healthy controls and 16 MA patients were collected to do 16S rRNA gene high-throughput sequencing analysis. The abundance of theBacteroidetes,Proteobacteria,Actinobacteria,Escherichia,Streptococcus_ Salivarius, andLactobacilluswas significantly reduced in the MA group, while, the abundance of theKlebsiellawas significantly increased in the MA patients. TheRuminococcaceaeand[Eubacterium]_coprostanoligenes_groupwere found only in the specimens of the MA patients. The Fabrotax function prediction analysis showed that four photosynthesis function bacteria (cyanobateria,oxygenic_photoautotrophy,photoautotrophy, andphototrophy) only existed in the MA group. In the analysis of the BugBase microbiome function prediction, theEscherichiaof the MA group is significantly reduced compared to that of the healthy controls in the items of thatContains_Mobile_Elements,Facultatively_Anaerobic,Forms_Biofilms,Potentially_Pathogenic.png,Gram_Nagative, andStress_Tolerant_relabundance. These alterations may affect the stability of the host's immune, neural, metabolic and other systems by interfering with the balance of the gut microbiota or by the metabolites of those bacteria, causing the MA. This study explored the possible pathogenic factors of the gut microbiota of the MA. The results provide evidence to figure out the pathogenesis of the MA.