Polar lipids in milk are receiving increasing interest due to their bioactivities. However, milk polar lipids present a wide range of physical–chemical properties at different concentrations, making their analysis challenging. In this study, we presented a comprehensive lipidomic method using ultraperformance supercritical fluid chromatography (UPSFC)-quadrupole-time of flight-mass spectrometry (Q-TOF-MS), which enabled the separation of 18 lipid classes (including nonpolar lipids, cholesterol, ceramide, glycerophospholipids, sphingomyelin, and gangliosides) within 10 min. The method was used to analyze the polar lipids in seven samples, including human milk, other mammalian milk and milk fat globule membrane ingredients, identifying 14 lipid classes containing 219 lipid molecular species. A mass spectrometry data processing strategy applicable for high-throughput studies was also developed and validated.