Objective To investigate the effects of repetitive transcranial magnetic stimulation (rTMS) on cognitive function and intestinal microflora in maintenance hemodialysis (MHD) patients with subjective cognitive decline (SCD). Methods 33 MHD patients with SCD at the First Affiliated Hospital of Xi'an Jiaotong University from July 2022 to July 2023 were selected and randomly assigned to an intervention group (rTMS group) and a sham stimulation group (Sham group) in a 1:1 ratio. The cognitive function and 16srRNA bioinformatics analysis of fecal DNA samples before and after the intervention were compared between two groups. Results After intervention, the MMSE score of the rTMS group was significantly higher than that of the Sham group (P=0.037), mainly due to differences in recall ability dimensions (P=0.039). After intervention, the SCD-Q9 score in the rTMS group was significantly lower than that in the Sham group (P=0.018), mainly due to differences in daily activity memory ability (P=0.037). After intervention, there was no significant difference in α-diversity and β-diversity between the two groups. After the intervention, the top five bacterial family in both groups all were Bacteroidaceae、Lachnospiraceae、Enterobacteriaceae、Ruminococcaceae、Prevotellaceae，accounting for about more than 75%. The top five bacterial genus in both groups all were Bacteroides、Escherichia-Shigella、Faecalibacterium、Prevotella、Roseburia，accounting for about more than 50%. LEfSe analysis was used to screen for the main differential microbiota. At the family level, there were 5 different microbiota among them, Marinifilaceae, Flavobacteraceae, RF39, Carnobacteriaceae were more abundant in the rTMS group, and Wohlfahrtiimondaceae was more abundant in the Sham group. There were 17 different microbiota at the genus level, with higher abundance of Faecalibacterium, and Odoribacter in the rTMS group, and higher abundance of Erysipelatoclostridium in the Sham group. Conclusion rTMS therapy may alter the cognitive function of MHD patients with SCD, enhance their memory ability, and regulate the differential microbiota associated with SCD, suggesting that this treatment may affect cognitive function during SCD by regulating the microbiota