The invention provides a microbial agent for solving physiological disorder problems of plant growing roots and a preparation method of the microbial agent. The microbial agent for solving the physiological disorder problems of the plant growing roots includes a secondary bacterial liquid of pseudomonas fluorescens, a secondary bacterial liquid of bacillus subtilis, a secondary bacterial liquid ofbacillus licheniformis, monosaccharide, potassium fulvate, amino acid and purified water and is obtained by mixing the secondary bacterial liquids obtained from secondary culture of bacterial strainsfor fermentation after primary culture and secondary culture. The microbial agent can be directly absorbed by the plant roots, improve soil characteristics, improve soil nutrients, decompose soil salt, promote growth and development of the plant roots and prevent the plant roots from being damaged by pathogenic bacteria; meanwhile, the microbial agent with multiple bacterial groups is obtained bycompounding three kinds of bacteria and conducting deep fermentation, has high compounding capability and can well adapt to the differences of actual production raw materials, prescribed quality standards can be satisfied without adding fertilizer raw materials, and the demands for large-scale commercialization can be met.