The overuse of copper-based fertilizers and pesticides over the last few decades has resulted in detrimental risks to our environment. Nano-enabled agrichemicals with a high effective utilization ratio have shown great potential for maintaining or minimizing environmental issues in agriculture. Copper-based nanomaterials (Cu-based NMs) serve as a promising alternative to fungicides. Three types of Cu-based NMs with different morphologies were analyzed for their different antifungal effects onAlternaria alternatain this current study. Compared to commercial copper hydroxide water power (Cu(OH)2WP), all tested Cu-based NMs, including cuprous oxide nanoparticles (Cu2O NPs), copper nanorods (Cu NRs) and copper nanowires (Cu NWs), especially Cu2O NPs and Cu NWs, showed higher antifungal activity againstAlternaria alternata. Its EC50were 104.24 and 89.40 mg L−1, respectively, achieving comparable activity using a dose approximately 1.6 and 1.9-fold lower. Cu-based NMs could introduce the downregulation of melanin production and soluble protein content. In contrast to trends in antifungal activity, Cu2O NPs showed the strongest power in regulating melanin production and protein content and similarly exhibited the highest acute toxicity to adult zebrafish compared to other Cu-based NMs. These results demonstrate that Cu-based NMs could offer great potential in plant disease management strategies.