Comprehending the biosensing mechanism of the biosensor interface is crucial for sensor development, yet accurately reflecting interfacial interactions within actual detection environments remains an unsolved challenge. An operando photoelectrochemical surface-enhanced Raman spectroscopy (PEC-SERS) biosensing platform was developed, capable of simultaneously capturing photocurrent and SERS signals, allowing operando characterization of the interfacial biosensing behavior. Porphyrin-based MOFs (Zr-MOF) served as bifunctional nanotags, providing a photocurrent and stable Raman signal output under 532 nm laser irradiation. Aptamer was used to bridge the Zr-MOF and the silver-encased gold nanodumbbells (AuNDs@AgNPs). The simultaneous in situ acquisition of target-induced PEC and SERS signal responses facilitated the correlation of electron transfer information from the photocurrent with the distance information from the SERS signal. It revealed the biosensing mechanism in which target-induced aptamer conformational bending drove the Zr-MOF to approach the electrode. However, the increase in charge transfer observed through conventional electrochemical methods contradicts the conclusions drawn from the operando PEC-SERS analysis. Comprehensive analysis indicated that redox probes introduced during the non-in-situ measurement process became adsorbed within the MOF pores, potentially affecting the judgment of the biosensing mechanism. In addition, the operando PEC-SERS biosensor simultaneously obtained two independent signals, providing self-verification to improve the accuracy and reliability of patulin detection. The linear ranges were 1 pg mL-1-10 ng mL-1 for the PEC method and 1 pg mL-1-100 ng mL-1 for the SERS method, respectively. This work provides a powerful tool for determining the interface characteristics of biosensors.