The invention belongs to the technical field of fecal microbiota transplantation, and particularly relates to a fecal microbiota capsule, as well as a preparation method and application of the fecal microbiota capsule. The preparation method comprises the following steps: (1) a fecal microbiota solution is prepared; (2) the fecal microbiota solution, obtained in the step (1), is added with a freeze-drying protective additive, and freeze drying is performed to obtain fecal microbiota freeze-dried powder; (3) a capsule is filled with the fecal microbiota freeze-dried powder, obtained in the step (2), to obtain the fecal microbiota capsule. Through adoption of the fecal microbiota capsule, flora is enabled to be comparatively concentrated and can be preserved for a long time at a low temperature; implementation of flora transplantation is facilitated, and invasive implementation manners, such as a gastroscope, an enteroscope and a nasointestinal feeding tube, are not needed; when the fecal microbiota capsule is applied to weak patients, the safety is increased.