Objective To overview the systematic review(SR) of efficacy and safety of fecal microbiota transplantation (FMT) in clostridium difficile infection (CDI). Methods PubMed, The Cochrane Library, EMbase, CNKI, VIP, WanFang Data databases and related website (http://scholar.google.com/) were electronically searched to collect SR and meta-analysis on FMT of CDI. The quality of collected documents and evidences were evaluated by OQAQ (Overview Quality Assessment Questionnaire) and GRADE (Grading of Recommendations Assessment, Development and Evaluation), respectively. Results Eleven SRs were included, in which 4 were completed by meta-analysis. The results of OQAQ showed that the score of one review was 2, the others SR received scores from 5 to 9. There were 9 SRs had reported the CDI clinical resolution rate (CRR), of which one SR showed CRR was 36.2%, and the others showed CRR were about 90%. Compared to upper gastrointestinal FMT, all studies showed lower gastrointestinal FMT (colonoscopy, enemas, etc.) had a higher CRR. The outcomes of selection and random fecal donor had no significant differences, and authors suggested that there should be made a standardization of donor screening table for safe fecal. Present evidence showed FMT were safety, and the majority of adverse events of FMT appeared to be mild, self-limiting and gastrointestinal in nature. The GRADE quality level of SR indicated from very low to moderate. Conclusion FMT, as a treatment for CDI, shows significant efficacy and safety, but need more high-level evidences because of its clinical translation difficulties. The study also give a reference to develop standardized clinical pathways of FMT to policy researchers.