The invention relates to a bio-organic compound fertilizer, which comprises the following components in part by weight: 10 to 30 parts of organic matter, 2 to 10 parts of compound microbial inoculants, 5 to 20 parts of humic acid, 5 to 20 parts of amino acid, 4 to 10 parts of chitin, 1 to 5 parts of polypeptide, 530 parts of nitrogen, phosphorus and potassium, 5 to 10 parts of secondary and trace elements, 5 to 15 parts of algae fertilizer, 5 to 10 parts of zeolite powder and 1 to 5 parts of synergistic agent. Through the scientific and rational formula, the bio-organic compound fertilizer achieves nutritive equilibrium and can satisfy the need of crop growth in nutrient. The microbial inoculants are added to quickly degrade natural macromolecular organic compounds into the organic fertilizer and decompose organic pollutants, which effectively improves the capacity of crops in the absorption of nutrient components, reduces the waste of the fertilizer and reduces the damage of the chemical fertilizer to soil to further achieve the nutritive equilibrium, satisfy the need of the crop growth in the nutrient, achieve the aims of low investment and high output value, improve the quality of the crops and improve the economic benefit brought by the crops.