Halide ion’s doping of fullerene core is crucial on the properties of highly conductive self-n-doped fullerene ammonium halides, which are a kind of promising electron transport material for photovoltaics. Herein, to understand their photoexcited electron transfer (ET) property, antimicrobial photodynamic inactivation (aPDI) activities of these materials were tested based on their unique electronic structure and bacterial electrokinesis. We observed that illuminated self-n-doped fullerene ammonium iodides (PCBANI and PCBDANI) could exhibit significant improvement of activity against two important plant pathogenic fungi, Sclerotinia sclerotiorum and Fusarium graminearum as electron donor, compared with that in dark. Through comprehensive studies, such as aPDI activity, hyphal cell morphology, ultrafast transient absorption spectroscopy, solid state nuclear magnetic resonance (ssNMR), level of total cellular reactive oxygen species (ROS), we verified that not ROS but I radical’s oxidative stress is responsible for the improved aPDI activity. Moreover, the photobiological activity of self-n-doped fullerene ammonium halides is dependent on the reducing capacity of halide anions. The ET rate from anion to an excited fullerene core decreased successively from I– to Br– and then Cl–, illustrating that the generation rate of I radical species was the fastest and consistent with the high activity of fullerene ammonium iodides. Remarkably, adding potassium iodide did not enhance PCBANI’s antifungal activity. These results disclose that the unique electronic structure of iodide and fullerene core in self-n-doped PCBANI aggregates are critical for its aPDI activity. Consequently, we propose a possible dual-redox cycles mechanism involving photoexcited fullerene radical anions and I radical species in self-n-doped fullerene ammonium iodide aggregate to exhibit sustainable aPDI activity. This work reveals that halide ions play an equally important role as fullerene core in photoexcited ET property of self-n-doped fullerene ammonium halides.