The invention relates to a method for preparing a high-concentration biological deodorant. The method uses natural plants and extracts thereof with deodorizing function, a carbon source, a nitrogen source, trace elements and the like as raw materials, screens special beneficial microbial strains, and ferments the strains to obtain the high-concentration deodorant containing active components of the plants, beneficial microbe and metabolic products by adopting modern bioengineering technology. After being diluted by clear water which is 2,000 times of the deodorant, the deodorant is directly sprayed; and by decomposing smelly substances such as ammonia, hydrogen sulfide, methyl mercaptan, trimethylamine and the like, the growth of harmful microbe generating bad smell in rubbish and smell sources is suppressed so as to achieve the purposes of removing bad smell, repelling flies and reducing disease spreading risk. The deodorant is used for deodorizing in rubbish transfer stations, landfill sites, breeding farms, public toilets, toilets and other rotten places. The deodorant breaks through the defect of low dilution factor of the conventional deodorant, and implements the diluting use of 2,000 times. The cost is reduced while achieving the first level of deodorizing effect, and the acute oral toxicity test shows that the deodorant belongs to a practical non-toxic deodorant product.