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Nitrogen controlled atmosphere (N-CA) was widely used to keep grains from pest infestation. However, there was few studies on the grain quality changes during re-aeration after N-CA storage, i.e. N 2 -re-aeration storage (NRAS). In this paper, quality changes of two varieties of rice (Oryza sativa L.) during NRAS was investigated. Moreover, a non-targeted metabolomics approach was employed to reveal the mechanisms of rice quality changes after NRAS. Compared with rice in conventional storage (CS), fatty acid values (FAVs) and malondialdehyde (MDA) contents of rice showed slower increase rates in NRAS before re-aeration (0–60 days), while displayed faster increase rates after reaeration (60–150 days). And NRAS had no obvious effect on pasting and texture properties of rice. Additionally, metabolisms that are sensitive to changes in storage atmosphere are screened out, such as glycine, 4-aminobutyric acid, gluconic acid, sorbitol, γ-linolenic acid and stearidonic acid. This work provided a new insight into the mechanisms of rice quality changes after NRAS and helped reserve corporation develop storage policy for rice storage. • The quality changes of rice during NRAS were studied for the first time. • FAVs and MDA contents of rice showed faster increase rates than CS after re-aeration. • Re-aeration had no obvious effect on pasting and texture properties of rice. • AntiOxidant-related metabolites significantly down-regulated after re-aeration. • The resistance of the rice to oxidative stress was weakened after re-aeration. [ABSTRACT FROM AUTHOR]