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Cationic polymers are prospective fungicidal agents for inhibiting plant diseases because of the controllability of their structure and properties. This study investigates the effect of the hydrophobic–hydrophilic balance on the antifungal activities of antimicrobial polymers against phytopathogenic fungi (Rhizoctonia solani Kühn AG-1­(IA)), the pathogen of rice sheath blight (RShB). A series of polydimethylsiloxane-polymethacrylate block copolymers containing quaternary ammonium salts (PDMS-b-QPDMAEMA, labeled as SnQm; n and m represent 1000th of the molecular weight of the PDMS and QPDMAEMA chain, respectively) were synthesized via anionic ring-opening polymerization and atom transfer radical polymerization (ATRP). The abilities of the quaternary ammonium salts to adsorb onto the surface of R. solani sclerotia and permeate the R. solani sclerotia were investigated on the basis of static water contact angles and fluorescence labeling. The results indicated that the moderately hydrophobic PDMS chain helped stabilize the attachment of the hydrophilic QPDMAEMA chain and then help it penetrate the R. solani sclerotia. Its antifungal properties toward R. solani were characterized by determining its minimum inhibitory concentration (MIC) and minimum fungicidal concentration (MFC) and the inhibition rate of R. solani sclerotia germination. The hydrophobic PDMS chains had a significant influence on the antifungal activities of amphiphilic SnQm against R. solani sclerotia. This work highlights the prospective application of amphiphilic antimicrobial polymers as antifungal agents for inhibiting plant diseases.