The invention provides a slow transit constipation marking microorganism and application thereof, and further provides a kit according to the marking microorganism, which comprises a reagent suitable for detecting at least one strain in the marking microorganism, the invention relates to a method for preparing a microbial marker, which is characterized in that the microbial marker comprises the following strains: clostridium harzianum, Lachnospiraceae bacteria 3157 FAA CT1, a new species, Erysipastoris bacteria, Erysipastoris bacteria 2244A, Gordoniapastoris, Akkermansia muciniphila and clostridium symbiosum, and the microbial marker comprises the following strains: the clostridium harzianum, the Lachnospiraceae bacteria 3157 FAA CT1, the new species, the Erysipastoris bacteria 2244A, the Gordoniapastoris bacteria 2244A, the Akkermansia muciniphila and the clostridium symbiosum. The abundance of the microorganism provided by the invention is remarkably different in healthy people and patients with slow transit constipation, and the microorganism can be used as a marker for detecting and/or treating slow transit constipation.