The invention relates to nano-herb micro-pills for removing poisoning and a preparation method thereof. The micro-pills comprises the following active components in percentage by weight: 2.8 to 3.2 percent of terminalia leaf, 5.8 to 6.2 percent of serissa serissoides leaf, 7.0 to 7.4 percent of olive leaf, 3.4 to 3.8 percent of mono maple leaf, 10.0 to 10.4 percent of wild chrysanthemum leaf, 39.8 to 40.2 percent of nano-silicon dioxide modified by organic ligand, 23.8 to 24.2 percent of microcrystalline cellulose and 5.8 to 6.2 percent of chitosan. The nano-herb micro-pills can effectively reduce contents of heavy metal elements and toxic substances, such as malachite green, nitrofurans, carbostyril and the like in eel bodies, contributes to the repair of eel livers, adopts pure plant components as raw materials without new residues in the eel organism, has high safety, and simultaneously meets the national requirement of environmental protection.