Difference in thermal stability of two commercially available canola oils prepared by either expeller-extraction (EE) or solvent-extraction (SE) method was investigated. After 5 days consecutive deep-fry, content of oxidized-triacylglycerols (oxTAGs) in SE oil increased by 250.0% compared to its original status. However, 62.5% increase of oxTAGs in EE oil occurred, indicating that EE oil exhibits superior thermal stability to SE oil. Antioxidant capacity of EE oil was highly retained and loss rate of tocopherols in EE oil was much slower than in SE oil during deep-fry. Lipidomics showed that although there was no significant difference in molecular profile of either triacylglycerols or diacylglycerols between two oils, EE oil was characterized with 19 times higher phosphatidylcholine contents than SE oil. Considering no difference in antioxidant capacity between the two oils in their original status, it is proposed that synergetic mechanism is simultaneously initiated by antioxidant compounds and phosphatidylcholines, which plays key roles for maintaining better thermo-stability of vegetable oil during deep-fry.