Multiple and sensitive mycotoxin detection is an essential early-warning mechanism for safeguarding human health, and preserving the environment. We synthesized a turn-on Fluorescence Resonance Energy Transfer (FRET) aptamer sensor based on the unique fluorescence quenching and substrate recognition characteristics of Ag NTs (energy receptors) and aptamer modified Fe3O4@TiO2 NP (energy donor) to detect multiple toxins using a single diagnostic approach. The addition of aflatoxin B1 (AFB1) and ochratoxin A (OTA) resulted in a change in fluorescence intensity at 510 and 650 nm, which can be employed for simultaneous recognition with detection limits of 0.94 ng·mL−1 (R2 = 0.997) and 0.54 ng·mL−1 (R2 = 0.995). The aptasensors have been successfully applied for the determination of AFB1 and OTA in grain and oil samples with high recovery rates. The approach provides novel possibilities for the development of sensitive and selective aptasensors with potential applications in aptamer-recognized multifunctional biosensing.