Change in metabolites and volatiles during yellowing process in six rice cultivars was analyzed. Based on the yellowness, the study indicated Japonica was more prone to yellowing than Indica rice. Metabonomics analysis showed most differential metabolites were up-regulated, in which pathways of flavone and flavonol biosynthesis were significantly enriched following the yellowing process. Meanwhile, 54 differential metabolites were overlapped in six comparative groups, which is characterized by commonly-shared metabolic regulation pathway in each rice. Phenylalanine content was increased, followed by the enhanced phenylpropanoids formation, showing transformation between primary and secondary metabolites during yellowing process. Furthermore, 43 volatile compounds were identified, and the yellowed rice had more volatiles, including ketones, alcohols, esters and hydrocarbons, suggesting a positive correlation with the yellowing. Compounds 6-methyl-5-hepten-2-one and 6,10,14-trimethyl-2-pentadecanone were increased steadily during yellowing process, which may be applied for monitoring rice yellowing progress. This investigation provides further insight for revealing rice yellowing mechanism.