The invention relates to the field of fertilizers and particularly relates to a fertilizer batching microbial agent and a preparation method therefor. The fertilizer batching microbial agent is characterized by being prepared from the following raw materials in percentage by weight: 35% to 50% of powdery composite microbial agent, 2% to 17% of trace elements, 30% to 45% of mineral matter powder and 18% to 33% of humic acid. The fertilizer batching microbial agent is applicable to the fertilizer batching of various fertilizers such as compounded fertilizers, organic and inorganic compounded fertilizers and organic fertilizers and can be used for effectively preventing moisture transfer between organic material granules and inorganic material granules so as to achieve that two or more kinds of material granules can be mixed according to any ratio; the phenomena of crushing, melting and the like of the granules caused by the moisture transfer among the granules do not occur during long-time placement, so that large-area mechanical sowing for farmers is facilitated, blending-while-using is not required, and the labor amount is reduced; and meanwhile, due to the fertilizer batching microbial agent, the utilization ratio of a batched fertilizer is increased, the consumption of the fertilizer is lowered, and the batched content of nitrogen, phosphorus and potassium is also lowered.