Bioactive components are nutrients in rice, and the lower milling processing helps minimize their loss. However, their state during rice storage remains uncertain. This study investigated the changes in the bioactive component content during rice storage after different degrees of milling (DOM) and the potential mechanism of component loss through lipid oxidation. After 4 weeks of storage, the average retention index of phenols, gamma-aminobutyric acid (gamma-GABA), and vitamin B1(Vit B1) across all samples was 65.24, 25.68, and 63.74%, respectively. Compared to un-milled (DOM = 0%) and over-milled rice (DOM = 10 and 12 %), low-milled rice (DOM = 3, 6, and 8%) showed a faster rate of component loss, increased lipid oxidation, and lower pH during storage. The degreasing storage verified that milling-induced lipid oxidation was key in component loss, exhibiting a significant negative correlation (p < 0.01). Due to the differences in the sensitivity of components to lipid peroxide radicals, gamma-GABA experienced the highest loss during the lipid oxidation process, followed by phenols and Vit B1. Reducing storage temperature and humidity alleviated lipid oxidation in low-milled rice, preventing secondary loss of bioactive components. These results provide new insights supporting moderate milling and the preservation of nutrients in rice.