To determine the toxic effect of three imidazole ionic liquids (IILs) in terrestrial monocotyledonous and dicotyledonous plants, three IILs (1-butyl-3-methyl-imidazole tetrafluoroborate, 1-butyl-3-methylimidazole hexafluorophosphate, and butyl-3-methylimidazolium bi- [(trifluoromethyl)sulfonyl] imide) were investigated using rice and capsicum as target toxicity models. In hydroponic experiments, increasing the concentration of the IILs led to a decrease in the seed germination rate, a decrease in the reduced stem and root lengths, and an increase in the inhibition rate of the stem and root lengths; in addition, as the concentration increased, the reducing sugar content of rice and capsicum seedling leaves and roots first increased and then decreased, while permeability of the cell membranes of the stems and roots of the two plants also gradually increased. In terms of the effects on these indices in rice, the ranking of these three IIL anions was [TF2N]- > [PF6]- > [BF4]-; in terms of the effects on capsicum, the sequence was [BF4]- > [TF2N]- > [PF6]-. These findings provide a theoretical reference for the next step in the synthesis and the use of green ionic liquids.