In this paper, novel cationic chitosan derivative possessing 1,2,3-triazolium and pyridinium groups was synthesized conveniently via cuprous-catalyzed azide-alkyne cycloaddition (CuAAC) and methylation. FTIR, H-1 NMR, and elemental analysis examined the structural characteristics of the synthesized derivatives. The antifungal efficiencies of chitosan derivatives against three plant-threatening fungi were assayed by hypha measurement in vitro. The determination showed that chitosan derivative bearing 1,2,3-triazolium and pyridinium displayed tremendously enhanced antifungal activity as compared with chitosan and chitosan derivative bearing 1,2,3-triazole and pyridine. Notably, the inhibitory indices of it against Colletotrichum lagenarium attained 98% above at 1.0 mg/mL. The results showed that N-methylation of 1,2,3-triazole and pyridine could effectively enhance antifungal activity of the synthesized chitosan derivatives. Besides, the prepared chitosan derivatives showed non-toxic effect on cucumber seedlings. This synthetic strategy might provide an effective way and notion to prepare novel cationic chitosan antifungal biomaterials.