Fecal microbiota transplantation (FMT) has been used in a wide variety of diseases. Many researchers hypothesize that the dysbiosis of intestinal microbiota plays an important role in the development of gut-derived infections; thus, FMT is a potential therapeutic target against multiple organ dysfunction syndrome (MODS). A 106-year-old male patient was initially diagnosed with cerebral infarction and pulmonary infection. During the course of hospitalization, the patient developed MODS. The patient received a single nasogastric infusion of sterile-filtered, pathogen-free feces from a healthy donor. Fecal samples were collected every two days post-infusion to monitor changes in the microbiota composition in response to treatment. After FMT, MODS and severe diarrhea were alleviated; the patient’s fecal microbiome diversity resembled that of the healthy donor’s fecal microbiome; moreover, his clinical symptoms improved remarkably with the changes in fecal microbiome. Additionally, no observable side effects were noted during FMT treatment. These findings warrant further investigation of FMT as a putative new therapy for treating microbiota-related diseases, such as MODS.