The invention discloses a compound microbial water-soluble fertilizer and a preparation method of the compound microbial water-soluble fertilizer. The fertilizer comprises the following components in percentages by weight: compound microbial fermentation liquid 20-30%, amino acid powder 27-30%, urea 5-9%, ammonium dihydrogen phosphate 5-10%, potassium sulfate 10-15%, secondary element and trace element 1-5%, and water 15-20%. The method comprises performing aerobic fermentation on brown sugar, water, soybean milk and enzyme microorganism to obtain the compound microbial fermentation liquid, sequentially adding the secondary element and trace element, ammonium dihydrogen phosphate and potassium sulfate into a container filled with water, stirring at 70-90 DEG C until the material is dispersed uniformly and free of particle aggregates, cooling to 40 DEG C, sequentially adding the amino acid powder, urea and the compound microbial fermentation liquid, stirring for dissolution, and adjusting pH to be neutral. The compound microbial water-soluble fertilizer of the invention is rich in nutrients and easily soluble in water, prevents soil from hardening, promotes the growth and development of crop, improves the yield and quality of crop, and is suitable for drip irrigation, flushing and spraying.