Objective: This study aimed to explore the impurity removal law of soybean lecithin concentrate, analyze and identify the substances that affect the transparency of soybean lecithin concentrate. Methods: Using food-grade soybean lecithin concentrate as raw material and light transmittance as the main evaluation index, the effects of ceramic membrane pore size, material-liquid ratio, solvent system （n-hexane, n-hexane-anhydrous ethanol） and solvent ratio on impurity removal of soybean lecithin concentrate were investigated. Moreover, the collected impurities and soybean concentrated lecithin before and after impurity removal were analyzed and identified by lipidomics. Results: In the system of n-hexane-anhydrous ethanol, the inorganic ceramic membrane with a pore size of 20 nm was selected, and the ratio of solid to liquid of food-grade soybean concentrated lecithin: n-hexane-anhydrous ethanol was 1∶3 and the ratio of n-hexane to anhydrous ethanol was 3∶1, which could effectively remove the particulate and fat-soluble impurities that affected its transparency. Moreover, the lipid-soluble substances affecting the transparency of soybean condensed lecithin were identified as sugar ester monogalactose diacylglycerol and derivative ester dimethyl phosphatidylethanolamine by lipid proteomics analysis. Conclusion: The nano-scale ceramic membrane can effectively remove impurities from concentrated soybean lecithin in the system of n-hexane and absolute ethanol, and the transparency of the prepared products is better than that of imported transparent soybean lecithin.