Screening green solvents to improve the solubility of insoluble pesticides in water is a significant development direction for pesticide formulations in the future. Amino acid ionic liquids (AAILs) have strong dissolution properties and are widely used in dissolution. In this work, the conductor-like screening model for real solvents (COSMO-RS) as a solvent screening tool was used to screen AAILs with good solubility for two insoluble fungicides (fludioxonil and cyprodinil) and the physicochemical properties (viscosity, density, and CMC) of AAILs were characterized. The results showed that the selected AAILs had good solubility effects on fungicides, wherein the solubility of fludioxonil and cyprodinil in 1-ethyl-1-methyl-pyrrolidinium glycinate ([Empy][Gly]) was 115.78 and 67.17 g/L, respectively. The mechanism of the AAIL dissolving the fungicide was explored by theoretical calculation and IR characterization, indicating that the hydrogen bond interaction was the main driving force for AAILs to dissolve fungicides. The solubilization effects of AAILs in different systems were explored, and the results showed that the solubilization effect in aqueous solution was positively correlated with the content of AAILs, which was not only related to the interaction between fungicides and AAILs, but also the formation of micelles as an essential factor. Moreover, the impact of the biosurfactant rhamnolipid (Rha) and AAILs on the solubilization effect was explored, and most AAILs demonstrated a synergistic solubilization effect after adding Rha, which was expected. Finally, the inhibitory effects of organic solvent adjuvant methanol and eight AAILs on wheat growth were measured. Three [Empy] ILs showed less inhibitory effects on wheat than methanol under the same concentration. The research results indicated that AAILs had a promising research prospect as cosolvents in pesticide formulations.