Imidazolium bromide ionic liquids such as 1-alkyl-3-methylimidazolium bromides ([AMIm]Br) and 1-alkyl-2,3-dimethylimidazolium bromides ([AMMIm]Br) are common-use organic salts. However, data on comparative toxicological effects of these ILs are lacking for fish. In this study, a combined experimental and theoretical approach was applied to compare and analyze the effects of these ILs on biochemical biomarkers in liver of Carassius auratus treated with different concentrations (2 and 20mg/L) for 3 and 16d. Changes in the activities of superoxide dismutase, catalase, glutathione peroxidase, and in the levels of reduced glutathione and malondialdehyde were detected, indicating that these ILs exhibit potential biotoxicity. The integrated biomarker response (IBR) index suggested that 1-hexyl-3-methylimidazolium bromide ([HMIm]Br), 1-octyl-3-methylimidazolium bromide ([OMIm]Br), 1-hexyl-2,3-dimethylimidazolium bromide ([HMMIm]Br), and 1-octyl-2,3-dimethylimidazolium bromide ([OMMIm]Br) showed the highest biotoxicity under different concentrations or exposure time, while 1-ethyl-3-methylimidazolium bromide ([EMIm]Br) always showed the least stressful power towards the test organism. Quantum chemical calculations (electronic parameters, frontier molecular orbitals, and Wiberg bond order) were also conducted to interpret the experimental results. Notably, some descriptors were correlated with the toxicity order. In addition, theoretical calculations provided some valuable information on metabolic pathways of these ILs, which may help to get better understanding on their environmental behavior and fate. In general, the toxicological determination and analysis of these ILs were performed with a combined experimental and theoretical method, which may contribute to the future ecotoxicological studies.