The invention discloses a compound biological feed additive and a preparation method thereof. The preparation method comprises a step (1) of selecting aspergillus niger, lactobacillus plantarum, bacillus licheniformis, saccharomyces boulardii and trichoderma to prepare a compound probiotics leavening agent; a step (2) of making molasses, ammonium citrate dibasic, K2HPO4, KP2PO4, magnesium sulfate-water (1/7), manganese sulfate-water (1/1), ferrous sulfate, zinc sulfate, sodium selenite, lipoic acid, sodium acetate, VB1 and water into culture solution; a step (3) of mixing the leavening agent and the culture solution, and obtaining a compound probiotic fermented liquid; a step (4) of mixing and then inoculating bean pulp, corn, bran and soy isoflavone crude extract; and a step (5) of adjusting moisture and performing fermentation to obtain the compound biological feed additive. The preparation method is simple, the content of soy isoflavone aglycone and beneficial microorganisms and metabolites thereof in the obtained compound biological feed additive is high, and the compound biological feed additive is non-toxic and free of medicine resistance and side effect.