The invention provides composite microorganism organic inorganic water-soluble fertilizer and a preparation method thereof and belongs to the field of agricultural fertilizer. The composite microorganism organic inorganic water-soluble fertilizer comprises urea, calcium superphosphate, potassium dihydrogen phosphate, potassium chloride, potassium sulfate, zinc sulfate, mixed microbial agent, compound plant extract, cane sugar and the like. The composite microorganism organic inorganic water-soluble fertilizer has the advantages that the organic-matter compound plant extract, the microbial agent and the like are added into the fertilizer, and the fertilizer is rich in microorganisms, algal polysaccharide, phenols, multi-polymer, mannitol, betaine, alginic acid, plant growth regulating substances and elements such as nitrogen, phosphorus, potassium, iron, boron, molybdenum and iodine, harmless to human and livestock, and capable of greatly reducing environment pollution and inhibiting bacteria, killing pests and preventing diseases; in addition, the fertilizer integrates fertilizer efficiency and functions of sterilizing and pest killing and is simple in preparation method, balanced in nutrition release, high in fertilizer efficiency, high in fertilizer utilization rate and evident in yield increasing effect.