Surface-enhanced Raman spectroscopy (SERS) is a robust analytical tool applicable for the quick and accurate determination of mycotoxins. However, there hasn't been any attempt to use SERS for the quantitative detection of nivalenol (NIV) thus far. To improve the Raman signals of NIV, we fabricated a polydopamine-coated silver nanoflower (PDA-AgNFs) SERS substrate with strong “hot-spots”. The PDA-AgNFs substrates showed superior SERS enhancement activities in the target analyte detection and quantification. It produced good substrate uniformity (relative standard deviation of SERS signals, RSD = 4.1% for substrate-to-substrate test, and 3.24% for spot-to-spot test), an enhancement factor of 2.87 × 106 towards rhodamine 6B (R6G), and detection sensitivity as low as 1 femtomolar (10−15 M) against R6G probe molecule. Moreover, the PDA-AgNFs SERS substrates were successfully used, for the first time, to detect NIV in corn, horse beans, and mushroom samples. The calibration curve showed a satisfactory linear fit based on the SERS intensities of different NIV concentrations. The detection limit (LOD) for the suggested approach was 0.22 nM (S/N = 3). Interestingly, the MTT assay experiment demonstrated that PDA-AgNFs had no toxicity against mammalian NIH-3T3 cells. The biocompatible PDA-AgNFs substrates with intense plasmonic effects and binding sites demonstrated impressive Raman enhancement, and could serve as an effective, label-free, and fast SERS-based analysis of NIV in real samples.