The invention provides an efficient breeding method of 4-androstenedione strains. The method includes the five steps of strain culturing, mutagenesis treatment, mutagenic strain culture solution coating and culturing, single colony inoculation and shaking table fermentation, and fermentation broth extraction and thin layer chromatography. By the adoption of the method, miniature fermentation tubes are used, thousands of miniature fermentation tubes can be cultured through one shaking table experiment, in this way, the number of cultured strains is increased per unit time, the culturing time for a preset number of strains is shortened, and then the efficiency of strain screening is improved. Meanwhile, because the miniature fermentation tubes are used, solvent can be directly added into the miniature fermentation tubes for extraction after fermentation is ended; in this way, the extraction steps are simplified, and operation time is shortened. In addition, the bi-phase thin layer chromatography method is adopted for replacing an efficient liquid phase method, an experimenter can detect hundreds of samples each day, in this way, the screening speed of the strains is increased, and the efficiency of strain screening is substantially improved.