Abstract: To investigate the quality changes of rice grains during storage and study the mechanism of its quality deterioration, Japonica rice (with an initial moisture content of 12.6%) was stored at 25℃, and its moisture content, whole refined rice ratio, germination rate, fatty acid value, catalase activity, and reactive oxygen species content during storage were monitored. The quality indicators of rice were measured according to the national standards. Targeted metabolomics was employed to compare the rice samples at the beginning and end of the storage period. The detection of metabolites were carried out by HPLC-MS/MS. The research revealed that the moisture content of the rice remained within the safe storage range throughout the storage period. The whole rice percentage, the germination rate, and catalase activity all exhibited decreasing trends. In addition, the fatty acid value and reactive oxygen species content of the rice significantly increased after storage. A total of 28 metabolites related to energy metabolism were detected using targeted metabolomics. Qualitative and quantitative analysis of these metabolites indicated that the tricarboxylic acid cycle and Embden Meyerhof Parnas pathway were strengthened, while the pentose phosphate pathway was weakened in rice cells after storage. The mechanism of quality deterioration during storage was that a large amount of reactive oxygen species were produced. Reactive oxygen species can regulate the energy metabolism in response to external environments. However, it was difficult to remove the reactive oxygen species by vitrue of the decrease of the antioxidant enzyme activity. The excessive accumulation of reactive oxygen species led to declines of rice processing quality and physiological activity. Safe and quality-preserved storage of rice grains is of great significance for ensuring food security. Research into the mechanism of rice quality deterioration during storage can provide a theoretical basis for proposing methods to delay rice quality deterioration.