Integrated physiological and proteomic analyses using japonica rice and glutinous rice were applied to investigate the proteome regulation related to rice yellowing during natural storage. The changes of soluble sugar and soluble protein combined with the up-regulation expression of related proteins indicated the enhancement of carbohydrate, protein and lipid metabolism in yellowed rice. The expression of heat shock protein was up-regulated, indicating that rice yellowing occurred under heat, dry or other abiotic stress. Nevertheless, this study noted that the rice yellowing might be associated with the emergence of secondary metabolites, because the gene ontology analysis showed that the biosyntheses of secondary metabolites and phenylpropanoid were significantly enriched in yellowed rice. Based on above results, a possible proteome regulation of rice yellowing is proposed in the current study.