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The scandal of detecting the flavoring solvent propane-1,2-diol (PD) in milk has brought a crisis to the trust of consumers in the dairy industry, while its deposition and transformation are still indistinct. Pseudo-targeted lipidomics revealed that PD accelerated the degradation of glycerolipid (33,638.3 ± 28.9 to 104,54.2 ± 28.4 mg kg −1 ), phosphoglyceride (467.4 ± 8.2 to 56.6 ± 4.2 mg kg −1 ), and sphingolipids (11.4 ± 0.3 to 0.7 ± 0.2 mg kg −1 ), which extremely decreased the milk quality. Recoveries and relative standard deviations (RSDs) of the established method were 85.0−109.9 and 0.1−14.9%, respectively, indicating that the approach was credible. Protein−lipid interactions demonstrated that 10 proteins originating from fat globules were upregulated significantly and the activities of 7 enzymes related to lipid degradation were improved. Diacylglycerol cholinephosphotransferase was the only enzyme with decreased activity, and the molecular docking results indicated that PD adjusted its activity through regulating the conformation of the active center and weakening the hydrogen bond force between the enzyme and substrate. This study firstly revealed the mechanism of deposition and transformation of PD in milk, which contributed to the knowledge on the milk quality control and provided key indicators to evaluate the adverse risks of PD in dairy products.