Background: Based on the 16S rDNA sequence, intestinal flora changes in atrial fibrillation (AF) patients were monitored, the correlation between the changes and CHA2DS2-VASC score was analyzed, and the possible related factors affecting the changes of intestinal flora were investigated. Methods: According to the inclusion criteria, 53 AF patients were selected as atrial fibrillation group (Group AF), detection of C-reactive protein (CRP), homocysteine (Hcy), total bile acid (TBA), brain natriuretic peptide (BNP), High-sensitivity cardiac troponin (Hs-cTn) and left ventricular ejection fraction (LVEF) were accomplished. A total of 29 healthy subjects who underwent physical examination with matched gender and age were selected as the healthy group (Group H), and the same examinations as in Group AF were handled. Structural composition of intestinal flora was detected and analyzed by 16S rRNA sequencing technology. Flora differences between Group AF and Group H were counted, and the correlation analysis among age, Hs-cTn, CRP, TBA, Hcy, BNP and LVEF were explored. Meanwhile, CHA2DS2-VASC score of 53 AF patients was fulfilled, then patients were divided into three subgroups according to different scores, namely: 0 point (AF-0, n = 9), 1 point (AF-1, n = 15), ≥2 points (AF-2, n = 29). Finally, the correlation of intestinal flora differences and CHA2DS2-VASC scores were analyzed. Results: In terms of Alpha diversity, compared with the control group, the abundance and diversity of flora in Group AF were observably reduced. However, at phylum and class level, there was no notable difference in community structure between Group AF and Group H (p > 0.05). Further statistics revealed that the composition and abundance of intestinal flora in Group AF were prominently different from those in Group H at phylum, class, order and family levels, which were correlated with CRP and LVEF. Additionally, bioinformatics analysis comparison was performed on three CHA2DS2-VASC score subgroups of Group AF with Group H. It was reported that at phylum level, the relative abundance of Firmicutes in Group AF-2 and Chloroflexi in Group H was higher. At class level, the relative abundance of Sphingobacteriia, Flavobacteriia and Alphaproteobacteria was higher in group H. At order level, the relative abundance of Sphingobacteriales, Micrococcales, Flavobacteriales, Sphingobacteriales and Rhizobiales in group H was higher. At family level, the relative abundance of Sphingobacteriaceae, Flavobacteriaceae and Clostridiaceae in group H was higher. At genus level, the relative abundance of Sphingobacterium in group H, Clostridiumsensustricto-1 in Group AF-2, Dialister and Allisonella in Group AF-1, and Prevotella-9 in Group AF-0 were higher. Conclusions: There were changes in the relative abundance of intestinal flora at phylum, class, order and family levels, which was concerned with LVEF and CRP value, whereas Alpha diversity index of the flora decreased. The composition and relative abundance of intestinal flora varied in AF patients with CHA2DS2-...