The invention discloses a traditional Chinese medicine living bacteria fertilizer master batch, a preparation method and a method for preparing fertilizer by using the master batch. The master batch comprises the following components: yeast, lactobacillus, photosynthetic bacteria, cellulose-decomposing bacteria, chinese mugwort, barbary wolfberry fruit, fructus amomi, crataegus and medicated leaven, Chinese yam, tuber fleeceflower root, malt, dried orange peel, areca seed, szechuan lovage rhizome, lysine, methionine and salt. The invention can be applicable to carry out secondary fermentation and activation treatment on the conventional fertilizers of plants or soil and lead the conventional fertilizer to become safe and reliable nutritional biological group carriers; and after entering the plant bodies or soil, under the effect of multiple factors, the carriers can automatically adjust the balance of fungus bodies in the plant bodies or soil, can enhance the growth of the plants and the soil improvement, strengthen the fertility of the soil and the disease resistance of the plants, and have safe use and no pollution to the environment.