The invention relates to a preparation method of a multi-functional soil organic water-retaining agent. Animal bone blocks and a vinegar humic acid liquid organic matter rich in source are reutilized,straw biochar is combined, and a specially made cross-linking fluid is utilized for preparing an organic water-retaining agent. Bones are semi-carbonized preprocessed so as to have adsorptivity and be increased in specific surface area without being completely carbonized, and the bones can fully adsorb organic matters and nutrient substances in a soak solution during a vinegar humic acid liquid soaking process. According to the water-retaining agent prepared by the invention, the water absorption capacity reaches up to 900, the water retaining rate reaches to 50 percent after 12h at 55 DEG C,the organic content is 28 percent, the gel strength is high, and the water retaining rate is larger than 90 percent after the water-retaining agent is centrifuged in a centrifugal machine for 30 minat 3000r/min; the nutrient releasing rate of the nutrient ingredients does not exceed 75 percent within 30 days; the multi-functional soil organic water-retaining agent is good for loosening soil, reproducing microorganisms, effectively improving a soil structure, and improving the permeability and the drought resistance of soil, non-toxic, harmless, green and environmental-friendly, so that a benign cycle is formed.