SARS-CoV-2 nucleocapsid protein (N protein) binds nucleic acids and packages viral RNA. DNA aptamers that specifically bind the N protein have been used in antigen-based COVID-19 detection and have potential clinical applications for preventing SARS-CoV-2 infection. However, the complex structures of the N protein with DNA aptamers and the mechanisms by which aptamers recognize the N protein remain unclear. Here, we report the NMR-derived complex structure of the N-terminal domain of the N protein (N-NTD) with a 58 nt DNA aptamer, A48. The complex structure reveals a distinct topology with a large contact area between A48 and N-NTD. The N-terminal intrinsically disordered region (IDR) of N-NTD forms close contact with A48, primarily stabilized by hydrophilic interactions. Deletion of the N-terminal IDR or substitution of positively charged arginine residues with negatively charged glutamate residues in the IDR region substantially reduced the binding affinity for A48. Because most previously determined N protein structures were obtained using constructs lacking the N-terminal IDR, this study reveals a topology of the N protein-nucleic acid complex and highlights the importance of the N-terminal IDR in nucleic acid binding.