The co-occurrence of mycotoxins in food represents a significant threat to human health, with aflatoxin B1 (AFB1), fumonisin B1 (FB1), and ochratoxin A (OTA) being among the most hazardous examples. Consequently, the development of reliable, multiplexed, and ultrasensitive methods for their integrated detection is essential for effective food safety monitoring. A three-channel microfluidic aptasensor has been constructed for concurrent determination of AFB1, FB1, and OTA with high sensitivity and specificity. This device incorporates an S-scheme heterojunction photoelectrode based on a metal-organic framework (MOF)-derived BiOBr@CdIn2S4 (M-BiOBr@CdIn2S4) composite, where CdIn2S4 nanosheets are uniformly anchored onto a tubular M-BiOBr framework. This configuration provides abundant sites for aptamer immobilization, promotes directional charge migration and enables efficient charge separation through rational band alignment, resulting in a stable and amplified photocurrent response. Upon toxin binding, the photocurrent decreases in proportion to the logarithm of the toxin concentration, providing a wide dynamic range: 5.0 × 10-5 to 5.0 × 101 ng mL-1 for AFB1, 5.0 × 10-3 to 5.0 × 103 ng mL-1 for FB1, and 5.0 × 10-4 to 5.0 × 102 ng mL-1 for OTA. The detection limits are as low as 1.7 × 10-2 pg mL-1, 1.6 pg mL-1, and 1.5 × 10-1 pg mL-1, respectively. The aptasensor demonstrates exceptional reproducibility, specificity, and stability within complex food matrices, thereby establishing a versatile platform for the rapid and ultrasensitive monitoring of multiple mycotoxins, which is crucial for safeguarding food safety and public health.