Provided is an application of natural faeces flora transplanting in intestinal disease treatment. Faeces of healthy people screened through multiple conditions is collected, intestinal canal mixed probiotic flora is collected through the steps of homogenating, suspending, diluting, filtering, centrifuging and the like and transplanted in the ways of a gastroscope, an enteroscope, a nose-jejunum tube, a fistulization opening, clysis and the like, flora balance in the intestinal canal is restored, and the effect of treating intestinal diseases is achieved. A method for treating bacteria with bacteria is adopted, the stability of the intestinal flora of a human body is maintained, a microecological treating method free of drug resistance and toxic and side effects is achieved, treatment is carried out in the mode of faeces bacterium capsules or bacterium liquid, and a good treatment effect is achieved on diarrhea, clostridium difficile infection, Crohn's diseases and the like.