The invention relates to the technical field of microbial fermentation, and discloses a method for fermenting a liquid fertilizer by using beneficial microorganisms. The method comprises the following steps: A, weighing the following raw materials in parts by mass: 11-14 parts of traditional Chinese medicine residues, 120-320 parts of a microbial fermentation agent, 2-8 parts of a nutritional agent, 50-90 parts of water, 35-45 parts of a solvent, 1-4 parts of a stabilizer, 3-9 parts of an additive, 16-24 parts of soybean meal, 1.5-2.5 parts of amino acid, 5-10 parts of rice bran and 3-8 parts of molasses, B, pouring the soybean meal, the rice bran, the amino acid and the traditional Chinese medicine residues into a container, uniformly stirring, adding water, and controlling the water content to be 62-68%. The microbial fermentation agent and the nutritional agent are added into the raw materials, balanced nutrients are provided for plants or crops, the raw materials are easy to obtain, harmless to soil and easy to decompose, and the bacillus cereus, the bacillus subtilis, the lactobacillus, the lactic acid coccus, the streptococcus faecalis and the bifidobacterium can degrade heavy metals such as lead, cadmium, mercury and arsenic, so that the soil activity is effectively improved; and the crop yield is improved.