Sclerotinia sclerotiorum, a fungus that causes a devastating fungal disease of rapeseed (Brassica napus), causes significant yield losses globally. Carbon dots (CDs), a class of carbon-based nanomaterials, have emerged as promising agents for plant disease management owing to low toxicity and biocompatibility. This study demonstrates the antifungal potential of Salvia miltiorrhiza-derived CDs in enhancing resistance to S. sclerotiorum in rapeseed. In vitro assays revealed concentration-dependent suppression of fungal growth by CDs. In planta applications triggered multifaceted defense responses evidenced by: (1) increased glucosinolate accumulation and redox homeostasis through ROS modulation and elevated superoxide dismutase/catalase activities; (2) transcriptional activation of ROS-scavenging systems and biosynthesis pathways for defensive metabolites (flavonoids and phenylpropanes); and (3) restoration of pathogen-impaired physiological processes, including photosynthetic recovery via Calvin cycle reactivation, energy metabolism through TCA cycle enhancement, and stress-responsive hormone signaling. Integrated multi-omics analyses further indicated that CDs establish a coordinated defense network by simultaneously optimizing metabolic homeostasis and amplifying disease resistance mechanisms. These findings position CDs as a novel eco-friendly strategy for biotic stress management, providing a sustainable approach to mitigate crop losses caused by fungal pathogens.