Although quaternary ammonium salts are widely used in plant antifungal agents, their toxicity and renewability remain challenges. In this study, we synthesized three types of rosin-based gemini quaternary ammonium salts (Rbs): ortho- (o-Rbs), meta- (m-Rbs) and para- (p-Rbs) gemini salts. These salts were then tested for their in vitro antifungal activity against various plant pathogens, including Valsa mali, Phytophthora capsici, Fusarium graminearum, Fusarium oxysporum f. sp. niveum, and Alternaria solani. All three quaternary ammonium salts all exhibited significant and persistent antifungal activity against the tested pathogens. Of these, m-Rbs demonstrated the strongest activity against V. mali (EC50 = 2.649 μg/mL). In in vivo antifungal tests, m-Rbs exhibited promising protective and therapeutic effects on apples. A combination of spectroscopic techniques, experimental results, density functional theory (DFT), and molecular docking simulations revealed that m-Rbs effectively disrupts the cell membrane structure of V. mali. This disruption accelerates the leakage of intracellular contents and electrolytes. Additionally, acute toxicity tests in mice revealed that the median lethal dose (LD50) of m-Rbs was 6484.198 mg/kg, classifying it as nontoxic according to standard toxicity evaluation criteria. Therefore, m-Rbs is one of the most promising antifungal agents for agricultural use.