This study compared various extraction methods to analyze the lipidomics of Malania oleifera seed oil. The lipid composition of Malania oleifera seed oil was characterized using ultra-high-performance liquid chromatography-Q-Extractive plus mass spectrometry for supercritical fluid CO₂-extracted oil (SCO), ultrasonic-assisted petroleum ether-extracted oil (UPO), and hydraulic press-extracted oil (HPO). A total of 38 lipid subclasses and 2964 lipid species were identified in all three extraction methods of Malania oleifera seed oils, of which triglycerides and diglycerides were identified as the predominant lipids. UPO (189,031.89 μg/g) demonstrated lipid extraction capacity comparable to that of HPO (203,001.61 μg/g). For glycerolipid, UPO had the highest content compared to SCO and HPO. This study revealed that the three extraction methods significantly influenced the lipidomic profiles of Malania oleifera seed oil. These differences may result in the non-determinacy of the oil products and downstream product processing.