Lipid profiles of mango kernels may vary with variety. This study aimed to investigate the lipid profiles of five mango kernels and identify differential lipids using a combination of lipidomics and chemometrics. Results showed that 9cC18:1 and C18:0 represented the predominant fatty acids in all sampled oils. The unsaturated fatty acids exceeded saturated fatty acids in Australian mango (AM), Hongyu mango (HYM), Jidan mango (JDM) and Tai mango (TM), whereas the opposite was observed in Qingpi mango (QM). A total of 900 lipids were identified. No significant differences in glycerolipids were observed among the five mango kernels. AM and JDM had the highest glycerophospholipids and saccharolipids contents. Correlation analyses revealed mostly positive correlations among lipid subclasses within the same major group. Furthermore, 175 differential lipid molecules from 25 subclasses were screened. Bioinformatics analysis suggested that glycerophospholipid metabolism was the most influential metabolic pathway, followed by glycerolipid metabolism. These findings provide insights into the nutritional value of mango kernel lipids and offer a theoretical foundation for their application in the industry.