Background Fecal microbiota transplantation(FMT) can improve and reestablish the normal function of intestinal flora. It has been shown to have great potential in the treatment of inflammatory bowel disease(IBD). Objective To assess the current status and analyse the factors influencing the acceptance of FMT treatment in IBD patients. Methods IBD patients were recruited at the Inflammatory Bowel Disease Center in Yunnan Province, China. Participants voluntarily completed a self-designed questionnaire and a Chinese version of the Acceptance of illness Scale(AIS) test under the premise of informed consent, to assess their attitudes toward FMT and acceptance of illness. Results Of the 310 patients surveyed, 70.6% and 29.4% have diagnosed ulcerative colitis and Crohn's disease respectively. Less than half of IBD patients (43.55%) were willing to undergo FMT, 2.90% refused, and 53.55% were unsure about it.The most preferred routes of FMT among IBD patients were oral fecal capsules (50.97%) and colonoscopy (21.94%). In addition, prior knowledge of FMT (OR = 3.986, 95% CI: 2.304–6.896, P < 0.001), previous experience with FMT (OR = 12.505, 95% CI: 2.454–63.717, P = 0.002) and illness acceptance (OR = 0.951, 95% CI: 0.917–0.987. P = 0.029) were independent influences on the acceptance of FMT treatment in patients with IBD. Conclusion This study suggested that the acceptance of FMT treatment with IBD patients still needs to be improved, and the confidence of treatment may be enhanced by strengthening cognition and sharing the surrounding successful cases with FMT treatment. Furthermore, attention should also be paid to patients with low acceptance of illness with IBD patients, which may be a potential population for FMT treatment.