In this study, a group of novel water soluble chitosan ammonium salts with halogens were successfully synthesized, including chitosan-bromoacetate (CSB), chitosan-chloroacetate (CSC), chitosan-dichloroacetate (CSDC), chitosan-trichloroacetate (CSTC), and chitosan-trifluoroacetate (CSTF), and their antifungal activities against three kinds of phytopathogens were comparatively estimated by hypha measurement in vitro, respectively. The fungicidal assessment revealed that the synthesized chitosan derivatives had higher antifungal activity than chitosan. Especially, the inhibitory indices of CSTC and CSTF against three kinds of phytopathogens were higher than 70% at 1.0mg/mL. Generally, the antifungal activity decreased in the order: CSTF>CSTC>CSDC>CSC>CSB>chitosan. Apparently, the order of antifungal activity was consistent with the electronegativity of different substituted groups with halogens. The substituted groups with stronger electronegativity could augment the positive charge densities of cationic amino groups by drawing more electrons from the cationic amino groups of chitosan ammonium salts, which demonstrated that the protonation of amino groups was significant for the antifungal activity of chitosan derivatives.