Edible oils oxidize during microwave heating, which may affect their nutritional value and safety. Exploring the oxidation mechanisms of unsaturated fatty acids in edible oils to determine which are suitable for microwave heating is therefore important. We used GC-MS, low-field NMR, and 1H NMR techniques to study functional-group oxidation, the unsaturated fatty acid change law, and the distribution and migration of protons in various functional groups of four common vegetable cooking oils during microwave treatment. We show that the acid values of sunflower, soybean, peanut, and corn oil increased by 14%, 31%, 36%, and 101%, respectively, while the concentrations of malondialdehyde increased by 115%, 664%, 158%, and 333%, respectively, and the peroxide value fluctuated with increasing microwave power. The C16:0 concentrations of all four edible oils increased by more than 50%, and the concentration of polyunsaturated fatty acids decreased by more than 30% during microwave treatment; hence sunflower oil is the most suitable of the above-mentioned oils for daily microwave heating. In addition, we recommend the use of three characteristic functional groups to monitor the oxidative changes undergone by oils: olefinic H (CH = CH), diallyl CH2 (CH = CH–CH2–CH = CH), and allyl CH2 (CH = CH–CH2).