The invention provides a compound microorganism fertilizer with a high nutrition content, and a preparation method thereof, and relates to the technical field of plant fertilizer. The compound microorganism fertilizer with the high nutrition content is prepared from the following raw materials: saccharomycetes, acetic bacteria, yield improvement bacteria, potassium humate, bacillus licheniformis,trichoderma koningii, bacillus megatherium, furfural residue, waste sugar solution, wheat bran, amino acid, microelement, nitramine phosphorus, urea sulfate, calcium magnesium phosphate, monopotassiumphosphate, potassium fulvic acid and magnesium citrate. According to the compound microorganism fertilizer with the high nutrition content, no environment pollution is caused, crop growth can be accelerated, crop quality is improved, the biological activity of soil can be improved, the substance circulation of a soil ecological system is accelerated, harmful cultures in soil can be effectively prevented from breeding, organic nutriments are provided, the physical and chemical structure of the soil is improved, and the contents of nutrition substances in the soil are improved.