For efficient growth under varying light and nutritional conditions, plants keep the balance of carbon/nitrogen ratio by complex interactions between carbon and nitrogen metabolisms. The upstream regulatory modules may also interact for the balance. Despite their importance in controlling plant growth and biomass production, the underlying regulatory mechanisms of the carbon/nitrogen interactions have been mostly uncharacterized. In the present work, we characterized the expression and regulatory networks of starch biosynthesis and nitrogen assimilation using public microarray data of Arabidopsis. We showed that granule-bound starch synthase (GBSS) and ammonium transporter (AMT1;2) have a common expression pattern with their potential transcriptional regulators over a day/night cycle. Approximately 50% and 25% of genes for starch and nitrogen metabolisms, respectively, were shown to be diurnally regulated in Arabidopsis leaves. Among them, GBSS and AMT1;2 showed marked expression patterns having maximum transcript levels in the first few hours of the light period. This pattern was also detected for CONSTANS-LIKE transcription factors, COL and COL7. In addition, the networks of GBSS, AMT1;2 and their potential regulators were suggested to be robust in other conditions, indicating the significance of this regulatory module. We further found that knockout of COL and COL7 significantly affect the induction of GBSS and AMT1;2 transcripts, providing evidence that two contrasting metabolic processes, starch biosynthesis and ammonium transport, are controlled by common upstream regulatory factors.