Yellowing is associated with the changes in rice quality during storage. This study revealed that the increased yellowness of rice was highly associated with the moisture content of rice during storage. The hysteresis loop formed by sorption and desorption curves showed that the water loss of japonica rice was the largest, suggesting the internal structure of japonica rice was more vulnerable to be damaged. The heat enthalpy of rice increased first, and then decreased during yellowing, indicating the changes in the corresponding rice structure. The changes in the moisture migration were monitored by low-field NMR, and the data showed that the content of tightly bound water decreased during yellowing, and the tightly bound water transferred to higher fluidity in medium moisture content (MMC) and higher moisture content (HMC) sample. The concentration of most esters, ketones and alcohols of rice was increased during yellowing in a lower moisture content (LMC) sample. This study revealed that the yellowing process could inhibit the release of some volatiles for MMC and HMC samples. The increased 1,2-dimethoxy-benzene and phenol in HMC sample during yellowing were the characteristic volatiles for the highest yellowed rice samples. This study may highlight the further understanding of rice yellowing mechanism.