The invention discloses an organic-inorganic compound fertilizer and a preparation method thereof. The organic-inorganic compound fertilizer comprises the following raw materials in parts by weight: 25-30 parts of green algae, 12-17 parts of humic acid, 7-12 parts of bagasse mortar, 8-12 parts of saw dust, 7-15 parts of vermiculite, 5-10 parts of filtration mud, 5-10 parts of yeast organic waste water concentrated liquid, 5-8 parts of cane slag, 2-5 parts of sugarcane top and 2-5 parts of microbial strain liquid. The amount of the compound fertilizer organic matter is large than or equal to 55 weight parts, the total amount of NPK inorganic matters is large than or equal to 12 weight parts, the amount of the moisture is less than or equal to 25 weight parts, the effective viable count is large than or equal to 2 hundred million / gram, and the pH is 5.0-8.5. The preparation method comprises the following steps: fermenting twice by using microbial strains; adding inorganic porosity vermiculite, evenly mixing, and naturally drying so as to obtain the organic-inorganic compound fertilizer. Biodegradable agricultural and industrial production waste water, waste slag and sugarcane top regeneration organic matters are fully utilized as the raw materials, thereby improving the acidity and basicity of soil, improving the cation exchange capability (CEC) of the soil, improving the utilization of fertilizer, promoting the growth of crop and increasing the yield of the crop. The organic-inorganic compound fertilizer has the advantages of good ecological benefits and circular economy benefits and can be used as an additional fertilizer for crops such as sugarcane, watermelon and the like.