Ethyl carbamate (EC) is carcinogen occurring naturally in fermented foods, while the EC formation pattern in Feng-flavor Baijiu during Mare Nectaris storage and magnetic field treatment remains controversial. In this work, variation of EC in Mare Nectaris and magnetic field were investigated for the first time through ultra high performance liquid chromatography quadrupole-orbitrap high resolution mass spectrometry (UHPLC-Q-Orbitrap). Quantification results revealed that EC decreased significantly in the stage of 3–9 years and kept at 12.4 μg L−1 after 10 years of aging. Arginine succinate synthase (ASS) and urease were deemed as vital factors for EC decomposition. Degradation effetc of EC in 250 mT is simillar to that of EC in Baijiu stored in Mare Nectaris for 8 years. This is due to that aging process was accelerated by magnetic field and the content of total acid in Baijiu was increased, creating a favorable environment for decomposition of EC and urea.