Functional constipation is a disease characterized by difficulty in defecation, reduced frequency of defecation, or a feeling of incomplete defecation, and does not meet the diagnostic criteria for irritable bowel syndrome. The incidence rate of the disease is high and the treatment is difficult, which seriously affects the quality of life of patients. Traditional treatment is mainly based on cathartic drugs, but long-term use can cause colon melanosis, intestinal nerve function damage, patient drug tolerance, and other issues, and the treatment effect is not satisfactory. The pathogenesis of functional constipation is complex, and recent studies have shown that it may be related to intestinal flora imbalance, mainly manifested by a decrease in specific anaerobic bacteria and an increase in some harmful bacteria and fungi. Fecal bacteria transplantation is a new type of special organ transplantation, which promotes intestinal peristalsis by reconstructing the structure of intestinal flora. This article reviews the mechanism of occurrence and development of fecal bacteria transplantation in the treatment of functional constipation, providing an effective reference for further clinical application of fecal bacteria transplantation.