This study systematically characterized the distinctive lipid profile of bovine milk from desert regions using lipidomics technology. By comparing milk samples from desert and non-desert areas, a total of 34 lipid subclasses and 845 lipid molecules were identified. The analysis revealed significant differences in lipid profiles between milk from desert and non-desert regions. Under the organic farming system, desert milk exhibited 46 significantly up-regulated and 29 down-regulated lipids compared to non-desert milk, while in the conventional farming system, 127 up-regulated and 86 down-regulated lipids were detected. Furthermore, the study identified 10 candidate lipid candidate biomarkers associated with milk from desert production regions, including specific phospholipid molecules with potential neuroprotective properties and sphingolipids associated with stress responses. Metabolic pathway analysis suggested that the differential lipids associated with desert and non-desert production regions were mainly involved in glycerophospholipid metabolism and retrograde endocannabinoid signaling. These findings provide a scientific basis for geographical indication certification and origin traceability of milk from desert production regions, and may also support the development of functional dairy products with region-specific nutritional characteristics.