The invention discloses a comprehensive bio-organic fertilizer capable of improving quality of agricultural products and a preparation method of the comprehensive bio-organic fertilizer, and relates to the technical field of agricultural fertilizers. The comprehensive bio-organic fertilizer capable of improving quality of agricultural products is prepared from, by weight, 45% compound fertilizer,fecal residue and waste water, bean pulp, crop straw, amino acid, calcium oxide, microelement, biological bacteria, swill, waste residues of fungi and composite additives. The preparation method includes the steps of (1) preparation of raw materials; (2), pretreatment of the raw materials, including pretreatment of bean pulp, swill and waste residues of fungi; (3), primary fermentation; (4), secondary fermentation; (5), tertiary fermentation; (6), drying; (7), mixing. The comprehensive bio-organic fertilizer has the advantages of neutralizing soil acidity, improving soil structure, removing hardened soil, improving contents of organic matters and microbial flora in soil, improving quality of agricultural quality and the like, and is applicable to planting of fruits and vegetables in the South of China.