The toxic effects of 1-octyl-3-methylimidazolium chloride ([C8mim]Cl) and 1-octyl-3-methylimidazolium bromide ([C8mim]Br) on wheat seedlings at 0, 1, 2, 4, 6, and 8 mg L−1 were studied on the 7th, 10th and 13th days of cultivation. In addition, the concentrations of [C8mim]Cl and [C8mim]Br in nutrient solutions were determined by high performance liquid chromatography for the first time. The results showed that the concentrations of [C8mim]Cl and [C8mim]Br in nutrient solutions were stable during the exposure period. However, the reactive oxygen species levels in the wheat seedling cells were enhanced after exposure to [C8mim]Cl and [C8mim]Br, which resulted in oxidative damage and lipid peroxidation. Additionally, the particular halide anion present in the IL compounds appeared to have little influence on the toxicity of ILs.