Photoelectrochemical (PEC) biosensors are usually based on the single photocurrent change caused by biorecognition events between analytes and probes. However, the photocurrent may be influenced by other factors besides target analytes and bring a false result. To improve the accuracy and reliability of PEC detection, here we proposed the design of a dual channel self-reference PEC biosensors. CdTe and CdTe-graphene oxide (GO) were chosen as the two PEC active material and modified onto two adjacent areas on the ITO electrode. Then they were functionalized with Aflatoxin B1 (AFB1) aptamer through covalent binding or physical adsorption, respectively. The cathodic current from CdTe-GO and anodic current from CdTe can be well distinguished by adjusting the bias voltage. With the simultaneous application of "signal on" and "signal off" model, dual concentration information may be obtained in one detection and serve as a reference for each other. By comparing these two results, this sensor can clearly distinguish whether the signal change was caused by AFB1 or other interference factors. Compared to traditional PEC biosensors, this design can provide a better accuracy and reliability, which is promising in the future development of PEC detection.