False positives are common and frequently occurring in detection of ochratoxin A (OTA) due to the complexity of the food matrix. In this paper, a novel bipolar electrode-electrochemiluminescence (BPE-ECL) sensing platform for sensitive OTA detection with one-step grain pretreatment was proposed. The biosensor uses cathode of closed BPE as a functional sensing interface and anode as a signal collection interface. On the functional sensing interface, the horseradish peroxidase (HRP) catalyze the polymerization of aniline to form polyaniline (PANI) on nucleic acid backbone which is supplied by DNA tetrahedron-structured aptamer (DTA) and hybrid chain reaction (HCR). In the presence of OTA, PANI is formed and can cause the change of ECL and luminescence voltage of the anode of BPE. On the signal collection interface, the Ru(bpy)32+/TPA system is used as ECL light output. In this way, the analyte does not need to participate the ECL reaction of the anode, which avoids direct contact of photoactive molecules with complex reaction systems and greatly reduce the influence of complex food matrix on signal acquisition. The accuracy of the BPE-ECL biosensor (one-step grain pretreatment) was similar with high performance liquid chromatography (HPLC) analysis (traditional national standard pretreatment method: GB5009.96–2016). Meanwhile, the BPE-ECL biosensor had higher sensitivity (LOD: 3 pg mL−1). Therefore, closed BPE could simplify sample pretreatment and improve detection capability.