The ubiquitous aflatoxin B1 (AFB1) contamination in foods and other complex matrices has brought great challenges for onsite monitoring. In this study, an ultrasensitive Nafion-immobilized functionalized multiwalled carbon nanotube (MWCNT)-based electrochemical (EC) immunosensor was developed for trace AFB1 detection. The introduced Nafion film could steadily stabilize functionalized MWCNTs with uniform distribution and tiling on the surface of a Au electrode. Functionalized MWCNTs with a large specific surface area, numerous active sites to couple with abundant anti-AFB1 monoclonal antibodies (mAbs), and high conductivity served as the signal amplifier for remarkably enhancing the sensing performance of the immunosensor. In the presence of AFB1, it was specifically captured by mAbs to reduce the amplified current signals, which were recorded by differential pulse voltammetry for the accurate quantitation of AFB1. Because of the synergistic effects of Nafion on the stabilization of functionalized MWCNTs as signal enhancers, the developed EC immunosensor exhibited an extremely high selectivity, excellent sensitivity with a limit of detection as low as 0.021 ng/mL, and a wide dynamic range of 0.05-100 ng/mL, besides fascinating merits of easy construction, low cost, good stability in 7 days, and good reusability. The anti-interference ability of the immunosensor was verified against three other mycotoxins, and the practicability and accuracy were confirmed by measuring AFB1 in fortified malt, lotus seed, and hirudo samples with a satisfactory recovery of 92.08-104.62%. This novel immunosensing platform could be extended to detect more mycotoxins in complex matrices to ensure food safety.