In this paper, a polyimide (PI)/Si/SiO2-based piezoresistive microcantilever biosensor was developed to achieve a trace level detection for aflatoxin B1. To take advantage of both the high piezoresistance coefficient of single-crystal silicon and the small spring constant of PI, the flexible piezoresistive microcantilever was designed using the buried oxide (BOX) layer of a silicon-on-insulator (SOI) wafer as a bottom passivation layer, the topmost single-crystal silicon layer as a piezoresistor layer, and a thin PI film as a top passivation layer. To obtain higher sensitivity and output voltage stability, four identical piezoresistors, two of which were located in the substrate and two integrated in the microcantilevers, were composed of a quarter-bridge configuration wheatstone bridge. The fabricated PI/Si/SiO2 microcantilever showed good mechanical properties with a spring constant of 21.31 nN/μm and a deflection sensitivity of 3.54 × 10−7 nm−1. The microcantilever biosensor also showed a stable voltage output in the Phosphate Buffered Saline (PBS) buffer with a fluctuation less than 1 μV @ 3 V. By functionalizing anti-aflatoxin B1 on the sensing piezoresistive microcantilever with a biotin avidin system (BAS), a linear aflatoxin B1 detection concentration resulting from 1 ng/mL to 100 ng/mL was obtained, and the toxic molecule detection also showed good specificity. The experimental results indicate that the PI/Si/SiO2 flexible piezoresistive microcantilever biosensor has excellent abilities in trace-level and specific detections of aflatoxin B1 and other biomolecules.