Phosphatidylcholine (PC) forms of EPA and DHA confer remarkable health benefits; however, effective enrichment methods remain underdeveloped. This study employed lipidomics techniques to investigate the elution patterns of PC molecules in column chromatography, aiming to prepare EPA/DHA-enriched PC derived from Antarctic krill oil. The optimal conditions for PC separation were identified as using 200–300 mesh silica gel, a 1:50 sample loading ratio, and a 3:2 dichloromethane-to-methanol solvent ratio, yielding a total recovery rate of 84.13 % and a purity of 97.32 %. Fatty acid analysis revealed that as elution progressed, the concentrations of EPA and DHA in the recovered PC gradually diminished, with the highest concentration observed in the initial PC fraction, reaching up to 76.16 %. Multivariate statistical analysis indicated that the elution order of PC molecules was influenced by their total carbon chain length and degree of unsaturation within the dichloromethane/methanol system. Notably, PC molecules containing two polyunsaturated fatty acid chains, such as PC 22:6/22:6, PC 20:5/22:6, and PC 20:5/20:5, eluted earlier, while those with shorter or less unsaturated fatty acid chains, including PC 16:0/18:1 and PC 16:0/16:1, eluted later. These findings offer valuable insights for the preparation of EPA/DHA-enriched PC, thereby advancing the development of marine PC-derived functional foods.