Elevated atmospheric CO2 concentration (eCO2) reduces nitrogen (N) content in rice plants and stimulates tillering. However, these are contradictory to the general consensus that reduced N would constrain rice tillering. To resolve this, we detected N distribution in organs and transcriptomic changes of different organs after subjected to eCO2 in combination with different N application rates. Our results indicated that eCO2 promoted rice tillers more under higher N supply conditions, and confirmed that N availability constrained tillering in the early growth stage. Despite N content declined in the leaf and sheath of rice exposed to eCO2, the new-born tillers had a stable or higher N content compared to those under ambient CO2. Apparently the redistribution of N within the plant per se was a critical adaptation strategy to eCO2 condition. Transcriptomic analysis revealed that eCO2 introduced less extensive alteration of gene expression than N application. Most importantly, the expression levels of multiple N-related transporters and receptors were differentially regulated, suggesting that multiple genes were involved in sensing the N signal and transporting N metabolites in adapting to eCO2. The redistribution of N in different organs could be a universal adaptation strategy of terrestrial plants to eCO2.