Breast milk plays a crucial role in the growth of captive giant pandas, particularly lipids crucial to brain, retinal, and central nervous system development. This study aimed to analyze the lipid differences among bovine milk, goat milk, and giant panda milk. Lipidomics was employed to conduct a comprehensive and systematic analysis of milk lipids from different animal sources. It enables rapid, high-throughput analysis and identification of the lipids present in the given material employing advanced instrumentation. Milk was analyzed through untargeted lipidomics. The results showed that giant panda milk was rich in phospholipids, including glycerophosphatidylcholines, glycerophosphatidylethanolamines, and glycerophosphatidylinositols, while bovine milk and goat milk were abundant in diacylglycerols and triacylglycerols (TAGs). The neutral and polar lipids in the three species showed that giant panda milk was richer in TAGs containing palmitic acid and sphingomyelins containing ultra-long-chain fatty acids. In the positive and negative ion modes, 223 and 128 significantly different lipids (SDLs) were found between bovine milk and giant panda milk, and 208 and 126 SDLs were found between goat milk and giant panda milk, which were highly correlated to five main pathways including sphingolipid metabolism, glycerophospholipid metabolism, metabolic pathways, glycerolipid metabolism, and inositol phosphate metabolism. Our work aimed to provide comprehensive lipid profiles of giant panda milk, bovine milk, and goat milk, and promote the development of giant panda milk alternatives.