As green and novel solvents, ionic liquids (ILs) are popular in many industries, which may threaten ecosystems. The effects of three imidazolium-based ILs with different alkyl chain lengths, including 1-octyl-3-methylimidazolium chloride ([C(8)mim]Cl), 1-decyl-3-methylimidazolium chloride ([C(10)mim]Cl), and 1-dodecyl-3-methylimidazolium chloride ((C(12)mim]Cl) on growth and photosystem of Arabidopsis thaliana were investigated. Root length, fresh weight, cell membrane permeability, and chlorophyll content of whole plant were significantly affected by ILs. Vein clearing, leaf chlorosis, and browning on the A. thaliana leaf abaxial surface occurred, with a dose-response relationship. The effect of ILs on whole plant increased with alkyl chain lengths. Chlorophyll fluorescence parameters of photosynthetic system II (PSII) were all affected in [C(8)mim]Cl and [C(10)mim]Cl treatments, electron-transfer was blocked, and photochemical energy conversion was damaged. There were no significant changes in chlorophyll fluorescence of newly-growing leaves in [C(12)mim]Cl treatment, but has severe effect on aged leaves. The number and size of starch granules and osmiophilic globules increased, plasmolysis and the chloroplast swelling occurred in [C(8)mim]Cl, [C(10)mim]Cl treatments and on aged leaves in [C(12)mim]Cl treatment, but no significant damages occurred on newly-growing leaves of [C(12)mim]Cl treatment, perhaps due to plant self-protection of plant. The results indicating the appropriate use of ILs is needed.