The invention discloses bio-organic fertilizer prepared from modeling clay slag as a main material and a preparation method thereof. The bio-organic fertilizer comprises, by weight, 85 to 90 parts of modeling clay slag, 15 to 20 parts of ammonium bicarbonate, 7 to 10 parts of cotton straw powder, 2 to 3 parts of cypress branch powder, 10 to 13 parts of pericarp, 1 to 3 parts of weathered coal, 3 to 4 parts of ammonium chloride, 7 to 9 parts of sesame cake, 2 to 4 parts of borax, 1 to 2 parts of chlorinated paraffin, 1 to 2 parts of potassium mineral powder, 4 to 5 parts of meerschaum powder, 64 to 70 parts of swill, 12 to 17 parts of brown sugar and 76 to 80 parts of human and animal dung. The bio-organic fertilizer has high organic content, improves soil quality, improves a soil structure, keeps an ecological balance, contains comprehensive nutrients, and contains macroelements and trace elements needed by crops, and a large amount of active substances produced in microbial fermentation.