The invention discloses a method for separating and preparing a high-purity Moxidectin membrane, and belongs to the technical field of pharmaceutical chemistry. The method comprises the following steps: performing membrane filtration on a pre-purified Nemadectin solution; after extraction with dichloromethane, removing solvents by using conventional concentration; successively performing a protection feeding reaction, an oxidation reaction, an oximation reaction and a protection removing reaction on concentrate to obtain a Moxidectin crude solution; filtering to remove impurities through a membrane separation technique; obtaining a high-purity Moxidectin concentrated solution through a membrane concentration technique. The method disclosed by the invention uses the membrane separation technique to replace column chromatography and a macroporous resin adsorption and separation method, the technique is stable, controllable, simple and practical, the industrialization is easy, the dosage of the solvents is reduced, and a high-temperature solvent removing process of a material solution is omitted, so that the degradation risk of products is reduced, the product purity, the product quality and the product yield are improved, at the same time, the energy resources are saved, and the production cost is reduced.