Deoxynivalenol (DON) is one of the most common mycotoxins in grains, causing gastrointestinal inflammation, neurotoxicity, hepatotoxicity and embryotoxicity, even at a low quantity. In this study, a facile electrochemical aptasensor was established for the rapid and sensitive determination of DON based on a multifunctional N-doped Cu-metallic organic framework (N–Cu–MOF) nanomaterial. The N–Cu–MOF, with a large specific surface area and good electrical conductivity, served not only as an optimal electrical signal probe but also as an effective supporting substrate for stabilizing aptamers through the interactions of amino (-NH₂) and copper. Under the optimal conditions, the proposed sensor provided a wide linear concentration range of 0.02–20 ng mL⁻¹ (R² = 0.994), showing high sensitivity, with a lower detection limit of 0.008 ng mL⁻¹, and good selectivity. The sensor’s effectiveness was also verified in real spiked wheat samples with satisfactory recoveries of 95.6–105.9%. The current work provides a flexible approach for the rapid and sensitive analysis of highly toxic DON in food samples and may also be easily extended to detect other hazardous substances with alternative target-recognition aptamers.