Although quinoa is nutritious, its high fat content and lipase activity make it easily oxidized during storage. Meanwhile, quinoa's lipid composition and changes during storage are still unknown. Therefore, we stored fresh quinoa flour at low temperature and low humidity (LL), normal temperature and normal humidity (NN), and high temperature and high humidity (HH) conditions for 120 days to assess its oxidative stability and to monitor the changes in lipid composition. Herein, the contents of fatty acids, the peroxide values, the malondialdehyde values, and the lipase activity in quinoa flour during storage are determined to evaluate its oxidation stability. At LL and NN conditions, the contents of fatty acids, the peroxide values, the malondialdehyde values, and the lipase activity changed slowly. They were 3 (LL) and 5 times (NN), 2.7 (LL) and 4.7 times (NN), 1.4 (LL) and 2.3 times (NN), and 1.5 (LL) and 1.6 times (NN) the initial content at storage up to 120 d. However, with the prolongation of storage time under HH conditions, they all increased significantly to 8, 6.6, 3, and 2 times the original content. Moreover, during the storage of quinoa under LL, NN, and HH conditions for 120 days, we continuously monitored the lipid composition of quinoa grains with UPLC-Q-Exactive Orbitrap MS/MS. We identified a total of 14 subclasses of 229 lipids, including 90 significantly different lipid species. PCA and PLS-DA showed that quinoa lipids in HH conditions changed significantly with prolonged storage; among these, the TG and DG classes were the most susceptible to oxidation, which could distinguish fresh quinoa from oxidized quinoa. Simultaneously, we also found that lipase activity has a significant impact on lipid metabolism through correlation analysis, which also indicates that enzyme inactivation treatment can slow down lipid hydrolysis and oxidation during storage. To explore the mechanism of these changes, we also identified twelve important lipid metabolism pathways during quinoa storage. In conclusion, our study advances knowledge of the storage stability and lipid oxidation mechanisms of quinoa and provides a theoretical basis for setting the shelf life of quinoa.