Objective To systematically evaluate the safety of fecal microbiota transplantation (FMT) for the treatment of recurrent Clostridium difficile infection (RCDI). Methods China National Knowledge Infrastructure (CNKI), China Biology Medicine (CBM), WanFang Data, PubMed, EMbase, Web of Science, The Cochrane Library Database were searched by computer, randomized controlled trials on FMT treatment for RCDI were searched, the search time limit was from the establishment of database to January 16, 2022. Meta-analysis was conducted after two researchers independently screened the literatures, extracted the data and evaluated the bias risk included in the study. Results A total of 11 studies were included, involving 756 patients. All 11 studies reported the occurrence of adverse reactions after FMT treatment for RCDI. Descriptive analysis was conducted on the specific values of 7 studies without adverse reactions. Meta-analysis results of the other four studies showed that: compared with treatment for RCDI with vancomycin or fidaxomicin, freeze-dried fecal microbiota, and fresh fecal microbiota, as well as comparison between fresh fecal microbiota and autogenous fecal microbiota, incidence of adverse reactions in patients receiving frozen fecal microbiota was no significantly different (all P>0.05). Conclusion The available evidence shows that FMT is safe and effective for the treatment of RCDI, and there is no direct correlation between the adverse reactions of patients and FMT.