In order to understand the dynamic changes of complex lipid contents in human milk during infancy, sequential window acquisition of all theoretical mass spectra (SWATH) with high acquisition hit rate assisted ultra-high performance liquid chromatography-triple quadrupole time of flight tandem mass spectrometry (UPLC-Triple-TOF-MS/MS) was used to identify and quantitatively analyze lipids in human milk at different lactation stages. The results showed that a total of 229 lipids were detected in human milk at the three lactation stages. According to the “Lipid Metabolism and Pathways Strategy”, five classes of lipids were identified: 1) glycerolipids (GLs) mainly including 24 diglycerides and 28 triglycerides; 2) glycerophospholipids (GPs) including 33 phosphatidylethanolamines, 21 phosphatidylcholines, 8 phosphatidylserines, 13 phosphatidylglycerols, 10 phosphatidic acids and 7 phosphatidylinositols; 3) 22 sphingolipids (SP); 4) 10 sterol lipids (ST); and 5) 4 fatty acids (FAs) and their derivatives. The relative contents of GL and SP increased gradually with lactation time, while the relative contents of GP, ST and FAs decreased gradually. This study achieved a comprehensive qualitative and relative quantitative analysis of lipids in human milk. The developed method is sensitive, precise and stable. It provides a basis for the development of infant food simulating human milk at different stages of lactation.