In recent years, sprouted seeds have attracted increasing global attention owing to their superior nutritional value. For instance, sprouted wheat flour exhibits greater contents of fiber, as well as certain vitamins and minerals, compared to all-purpose flour. Meanwhile, sprouts are considered one of the most contamination-prone fresh produce items and have been recognized as a major source of foodborne pathogen outbreaks, thereby presenting a serious food safety issue. Photosensitization is a promising eco-friendly method to control microorganisms in cereal grains. Our previous study demonstrated that curcumin, as a natural photosensitizer, can inhibit Fusarium fungal growth and mycotoxin production in vitro. Therefore, this study aimed to evaluate the effectiveness of several natural photosensitizers (PSs) for decontaminating Fusarium head blight (FHB) infected wheat grains and sprouted wheat grains including curcumin, coumarin, and menadione sodium bisulfite (MSB). Initially, the specific fungal species contaminating FHB infected wheat were identified through sequencing and subsequently confirmed by comparing the sequences against the NCBI nucleotide database using Basic Local Alignment Search Tool (BLAST). The results showed that the fungi present on FHB infected wheat included Arthrinium sp., Aspergillus sp., Fusarium graminearum, Alternaria alternata, and Cladosporium sp. Afterwards, the three aforementioned natural PSs were evaluated for their ability to decontaminate wheat seed surfaces by counting surviving fungal colonies on 100 FHB infected wheat seeds. The antifungal results indicated that curcumin and coumarin, combined with light treatment, completely inhibited fungal colony growth at concentrations of 3 mM and 4 mM, respectively. In contrast, 4 mM of MSB significantly inhibited fungal growth as compared to control, but less effective than that of curcumin and coumarin. In terms of mycotoxin suppression in wheat seeds and sprouted wheat seeds, all three natural photosensitizers (p < 0.05) significantly reduced overall mycotoxin production. Among them, MSB effectively reduced all tested mycotoxins (DON, 3-ADON, 15-ADON, Nivalenol, T-2, and Zearalenone), while curcumin and coumarin only significantly reduced DON, Nivalenol, T-2, and Zearalenone. Additionally, the effects of the three photosensitizers on seed germination rate were evaluated. The results indicated that coumarin and MSB did not affect germination rate, whereas curcumin significantly reduced the germination rate of wheat seeds as compared with control sample. In conclusion, MSB based photosensitization treatment shows great potential for controlling fungal contamination and mycotoxin production in highly contaminated wheat seeds and germinated wheat sprouts.