Aflatoxin B1 (AFB1), one of the most toxic mycotoxins, has undergone a wide range of studies over the years. The development of rapid, simple, and sensitive analytical methods remains a major challenge for the accurate detection of AFB1 in foodstuffs. In this study, we designed an enhanced and stable ingenious electrochemiluminescence bioaptasensor (IEC-BA) for ultrasensitive detection of AFB1 based on the synergistic effects and enzyme-driven programmable assembled 3D DNA nanoflowers (EPDNs). This synergistic effect was comprised by the competitive impact on auxiliary probes (AP) and the cutting effect of the Hae III. Compared to the traditional aptamer directcompetition method, the synergistic effects ensured that the aptamer was more efficiently and adequately competed away by the target. Also, the redundant double-stranded probes were removed, which greatly facilitates simple, quick, and sensitive detection of AFB1. Besides, a large chunk of positively charged Ru(II) complexes (Ru(bpy) 3 2+ ) was accumulated by the utilization of EPDNs, which resulted in tremendous improvement of the sensitivity of the designed method. Thus, even in the presence of trace amounts of AFB1, a sharply visual electrochemiluminescent signal was generated. The proposed method can realize the quantification of AFB1 with a good linear range from 1 ppt (pg mL −1 ) to 5 ppb (ng mL −1 ) with a detection limit of 0.27 ppt. In addition, it can also be successfully applied for the analysis of AFB1 in a peanut and wheat, with total recoveries ranging from 93.7 to 106.6%. Furthermore, the IEC-BA also exhibited good selectivity, reproducibility, and stability, revealing prospective applications of food safety monitoring and environmental analysis.