The invention belongs to the technical field of natural drug isolation and purification and relates to a natural L-alpha-glycero-phosphatidylcholine preparation method. The method includes: using acid liquor for soaking macroporous cation exchange resin, draining the acid liquor, washing with water, soaking with alkali liquor, washing with water, soaking with acid liquor again, washing with deionized water and using low-carbon alcohol for replacement; adding powder phospholipid into the low-carbon alcohol, alkalifying for reaction, leaching, washing with the low-carbon alcohol, adjusting pH to be alkalescent, decomposing, condensing, cooling, transferring into a separating funnel, standing, and separating out a lower-layer low-carbon alcohol phase; packing the powder phospholipid and the alcohol-phase resin, adsorbing alcoholysis mixed solution, washing the resin with low-carbon alcohol to remove impurities; and eluting the resin with pure water; and decolorizing with decolorizing agent, decomposing and condensing to obtain a finished product. The natural L-alpha-glycero-phosphatidylcholine preparation method has the advantages that process steps are simple, and industrial production requirements are met; resources are saved and cost is reduced; and the total yield of the finished product reaches 65.47-86.08%, the external standard content is more than 99%, and the optical purity is up to 99%.