In this study, nine pyrimethanil ionic liquids (PILs) were synthesized through an acid−base reaction with nine naturally derived organic acid anions to improve the physicochemical properties and reduce the environmental adverse impacts. The PILs presented lower volatilization, higher photostability, better soil adsorption capacity, and improved fungicidal activity relative to pyrimethanil. When the length of the carbon chains in the anions was increased, the PILs showed better properties in terms of melting point, water solubility, volatility, and surface tension. The photostabilities and fungicidal activities of the PILs were significantly improved when cyclic compounds were used as the paired anion ions. With enhanced physicochemical properties and better fungicidal activity, PIL7 was selected as the best alternative to pyrimethanil. The intrinsic disadvantages of pyrimethanil could be surmounted using the system developed in the study; thus, ILs could have immense potential in the development of eco-friendly and efficient fungicides in the future.