This study aimed to evaluate the impact of conventional (pressing extraction [PSE], solvent extraction [STE]), and non-conventional (microwave-assisted solvent extraction [MSE], subcritical fluid extraction [SBFE], supercritical fluid extraction [SPFE]) techniques on the quality of pecan oil using foodomics. The results indicated that MSE, STE, and SBFE yielded higher oil quantities. SPFE selectively extracted free fatty acids, leading to a higher acid value. MSE-derived oil exhibited the highest oxidative stability index. A total of 844 lipid molecules were identified, with glycerolipids and glycerophospholipids as the predominant classes. MSE and SBFE showed superior efficiency over conventional methods for the extraction of glycerophospholipids and saccharolipids. Additionally, 48 volatile compounds were identified, predominantly aldehydes and esters, with seven recognized as key aroma contributors. Dimethyl trisulfide had the most significant impact on the overall aroma. These findings offer a theoretical foundation for the efficient and sustainable production of pecan oil.