Ochratoxin A (OTA) is a prevalently toxic mycotoxin in agro-products and foods. Therefore, the development of highly sensitive analytical methods is extremely important for OTA determination. Herein, a label-free electrochemical aptasensor based on the tetrahedral DNA nanostructure (TDN) was fabricated for the detection of OTA and compared with an aptasensor based on complementary DNA (cDNA). With the introduction of TDN, the aptamers were vertically anchored on the AuE surface resulting in reduced entanglement and non-specific adsorption. Under optimal conditions, this TDN-based aptasensor exhibited a low detection limit of 0.68 ng/L with a broad linear range of 1–8000 ng/L. In comparison with the cDNA-based aptasensor (15.64 ng/L), the sensitivity was enhanced by 23 times, which demonstrated that the TDN was capable of facilitating the recognition between aptamers and OTA, giving rise to an improvement of the sensitivity. In addition, the practicability of this aptasensor was validated by determining wheat flour samples, which exhibited the comparable reliability to the ultra-high performance liquid chromatography (UPLC) method. This proposed strategy illustrated high sensitivity, specificity, reproducibility and stability, indicating its promising potential application in other contaminants.