The changes in storage quality and microstructure of brown rice with different moisture contents were investigated under low-temperature conditions. Three types of brown rice with different initial moisture contents of 13.5%, 15.5%, and 17.9% were studied under two storage conditions: 10%O2+90%N2 controlled atmosphere storage and air-natural sealing storage at 15 ℃. The results showed that, at 15 ℃, higher initial moisture content led to greater fatty acid values, lower germination rates, lower flavor values, and poorer microstructure in brown rice. Low-temperature controlled atmosphere storage delayed the increase in fatty acid values and the reduction in germination rates, thereby maintaining the quality of brown rice to some extent. This study provides a potential solution for the quality preservation and freshness storage of brown rice.