The invention relates to a method for preparing a prostaglandin E1 lipid microsphere injection of a charging non-homogeneous phase (comprising a water phase, an oil/water interfacial film phase and an oil phase) dispersion system, of which the surface of the lipid microsphere can be charged with positive electricity or negative electricity. The prostaglandin E1 is alprostadil, of which the chemical structure comprises a basic skeleton of 20-carbon fatty acid with a 5-carbon ring and two side chains, wherein one side chain is provided with a hydrophilic carboxylic acid group, so that the prostaglandin E1 has the characteristic of light surface activity action. By utilizing the characteristic, and according to the formula and the preparation process provided in the invention, the prostaglandin E1 has an unique drug-carrying mode in a solution of lipid microsphere with the non-homogeneous phase dispersion system, and the prepared lipid microsphere injection is fundamentally different from an alprostadil injection(Kaishi, and is prepared by adopting the technology of the Japanese business corporation LTT Bio-Pharma Co., Ltd. already sold in markets, and the difference lies in that the drug-carrying mode is completely different, the content of degradation products in the preparation such as impurities is more than 50 percent lower than that of in the Kaishi, so that the prostaglandin E1 lipid microsphere injection and the alprostadil injection are fundamentally different. The invention relates to a method for preparing the prostaglandin E1 lipid microsphere injection and the drug-carrying characteristics thereof in a three-phase system; in the formula, 0.0001 to 0.1 weight portion of prostaglandin E1 is used as a drug, the prostaglandin E1 is added with auxiliary materials for medical purpose to prepare the prostaglandin E1 lipid microsphere injection, and the auxiliary materials for medical purpose comprises the following materials in portion by weight: 5 to 20.