Storage was an essential part of brown rice circulation. During the storage process, the metabolic activity of brown rice was still ongoing, and long-term storage lead to the deteriorate of brown rice. Metabolomics analysis was performed using GC-MS to investigate the changes in metabolites of brown rice after storage at 18 °C for 12 months.In terms of quantity, sugar, fatty acids and other metabolites in brown rice decreased after storage, and alcohols, aldehydes, phenols and amines increased. A total of 34 differential metabolites were screened, In terms of content, the content of carbohydrates, amino acids, and fatty acids of brown rice decreased after storage, while the content of sugar alcohol, amines, and aldehydes increased after storage. Cluster analysis found that the low-expressed metabolites in the 0 storage time samples sample became highly-expressed after storage. While, highly expressed metabolites in the 0 storage time samples became low-expressed after storage. Metabolic pathway analysis showed that storage significantly influenced the lipid metabolism in brown rice. Palmitoleic acid, cholesterol, linoleic acid, and lauric acid are four key metabolites in lipid metabolism during storage of brown rice.Significant changes in quantity and type of brown rice metabolites after storage. Storage has the greatest effect on lipids. storage caused a "reverse change" in the metabolites content of brown rice. The obtained results may help in understanding the changes in metabolites profile and delaying of quality deterioration of brown rice during storage. This article is protected by copyright. All rights reserved.