Diurnal physiological acclimation regulated by a circadian system is an advantage for plant fitness. The circadian system is composed of a signal input, the clock and output pathways. Understanding the regulation mechanism of the output pathways remains a major challenge. Diurnal proteomic change reflects the state of circadian organization. We found the content of glucose, fructose, sucrose and starch diurnally changed in leaves of rice seedlings grown under a 12-h light/12-h dark condition with constant temperature. Dynamic proteomics analysis revealed 140 protein spots with diurnally changed levels at six times of the light/dark cycle; 132 spots were identified by MS, and 119 spots were of a single protein each with functional annotation. These proteins are involved in regulation of carbohydrate flow, redox, protein folding, nitrogen and protein metabolism, energy conversion, photorespiration and photosynthesis. Of these proteins, 81.5% were upregulated during the light phase, over-lappingly, 41.2% showed behavior of circadian anticipation to dawn. Pattern analysis showed that the diurnal regulation involved pathways of allocation of carbohydrates between temporary reserves and consumption, maintenance of redox homeostasis, diurnal protein reassembly and nitrogen assimilation. These pathways reflect biochemical phenotypes of the circadian change linking the oscillator and circadian outputs.