The invention discloses berberine and a berberine forming salt enteric micropellet, a preparation method and application thereof in preparing medicines for treating various metabolic diseases such ashyperglycemia, hyperlipemia, obesity and fatty liver. The berberine forming salt enteric micropellet includes a blank pellet core, a drug layer, a barrier layer, an enteric layer, and a protective layer from the inside to the outside. The drug layer includes the berberine and / or a salt which can be formed by the berberine, a dispersing agent, a binder, and a surfactant. The preparation method of the berberine forming salt enteric micropellet is a fluidized bed air suspension method or a droplet spray drying method. The berberine forming salt enteric micropellet prepared by the method can coverthe bitter taste of the berberine, reduces the simulating effect of the drug on gastric mucosa, reduces the adverse reaction of clinical use, improves the compliance of patients, is hardly released in stomachs, is rapidly released after entering the intestinal tract, has high bioavailability, and is suitable for the treatment of the hyperglycemia, the hyperlipemia, the obesity, the fatty liver and other metabolic diseases.