Abstract Here, deep sequencing results of the maize transcriptome in leaves and roots were compared under high‐nitrogen (HN) and low‐nitrogen (LN) conditions to identify differentially expressed circRNAs (DECs). Circular RNAs (circRNAs) are covalently closed non‐coding RNA with widely regulatory potency that has been identified in animals and plants. However, the understanding of circRNAs involved in responsive nitrogen deficiency remains to be elucidated. A total of 24 and 22 DECs were obtained from the leaves and roots, respectively. Ten circRNAs were validated by divergent and convergent primers, and 6 DECs showed the same expression tendency validated by reverse transcriptase‐quantitative PCR. Integrating the identified differentially expressed miRNAs, 34 circRNAs could act as miRNA decoys, which might play important roles in multiple biological processes, including organonitrogen compound biosynthesis and regulation of the metabolic process. A total of 51 circRNA‐parent genes located in the genome‐wide association study identified loci were assessed between HN and LN conditions and were associated with root growth and development. In summary, our results provide valuable information regarding further study of maize circRNAs under nitrogen deficiency and provide new insights into screening of candidate genes as well as the improvement of maize regarding nitrogen deficiency resistance. CircRNA–miRNA–mRNA co‐expression networks were constructed to explore the circRNAs that participated in biological development and nitrogen metabolism.