Penicillium italicum (P. italicum), a citrus blue mold, is a pathogenic fungus that greatly affects the postharvest quality of citrus fruits with significant economic loss. Our previous research showed that 2-methoxy-1, 4-naphthoquinone (MNQ) inhibited the growth of Penicillium italicum. However, the water dispersibility of MNQ will limit its further application. Herein, we synthesized MNQ-based carbon dots (2−CDs) with better water dispersibility, which showed a potential inhibitory effect on P. italicum (MIC = 2.8 µg/mL) better than that of MNQ (MIC = 5.0 µg/mL). Transcriptomics integrated with metabolomics reveals a total of 601 differentially enriched genes and 270 differentially accumulated metabolites that are co-mapped as disruptive activity on the cell cytoskeleton, glycolysis, and histone methylation. Furthermore, transmission electron microscopy analysis showed normal appearances and intracellular septum of P. italicum after treatment. These findings contribute tofurther understanding of the possible molecular action of 2−CDs.