Yellowing of rice during storage is a highly concerned issue for managing rice quality whereas the yellowing mechanism is not clearly elucidated so far. Thus, the comparative untargeted metabolomic analysis was performed in this study. The results revealed that glycolysis pathway and tricarboxylic acid cycle (TCA) were significantly enhanced in yellowed rice, indicating the activated energy metabolism was trigged during the yellowing process. In addition, the increased aromatic compounds (4-hydroxycinnamic acid and benzoic acid) and their precursors (phenylalanine, tyrosine) suggested the activation of shikimate-phenylpropanoid biosynthesis in yellowed rice, which is an antioxidant defense related pathway. In particular, the pathways involved in the metabolism of glutamate and arginine also significantly altered in yellowed rice. Therefore, the enriched pathways of increased amino acids, sugars, sugar alcohols, and intermediates of the TCA cycle during yellowing process are proposed to be associated with the response of heat and dry induced by the yellowing process.