Ionic liquids are remarkable chemical compounds, which are widely used in catalysis, energy, material preparation, biochemical and pharmaceutical fields due to their non-volatile, non-flammable, designable structure and high stability. In 1914, the first ionic liquid [EtNH3][NO3] was reported, but that was very unstable in the air. With the explosion, the development of ionic liquids has gone through a long period of silence. Subsequently, with the synthesis of chloroaluminate ionic liquids, the development of ionic liquids has become rapid, from imidazole, quaternary ammonium, pyridine-type ionic liquids to currently highly concerned functional ionic liquids. With the mass production and wide application of ionic liquids, their health risks to the environment have also attracted considerable attention. Although ionic liquids are green, stable, non-volatile, and non-flammable, which would not cause atmospheric pollution, they might be exist in soil and water environment in the process of use, such as production, recovery and treatment. In this paper, the structures of ionic liquids were described, and the influence of ionic liquids structure on biological safety was analyzed. The migration and transformation behavior of ionic liquids in different environmental media and the possible influencing factors were discussed. The environmental behavior of ionic liquids in water and soil is a systematic project. Single toxicity data and environmental data cannot objectively evaluate it. At present, a few related safety numbers of ionic liquids are available, and we should pay greater attention to the safety research of toxicity, degradation and corrosiveness directly related to environmental protection. The effects of ionic liquids on microorganisms, aquatic organisms and terrestrial organisms were summarized. There is no uniformity in toxic activities exhibited by ionic liquids. Some of them demonstrate relatively low toxicity, whereas others impose significant inhibitory effects in various biological systems. Several researches have been aimed at finding relationships that link the ionic liquid structure to its toxicity. However, no general correlations have been discovered. According to the accumulated data, the effect factors of toxicity are including the length of alkyl side chain in the cation, the presence and nature of functional groups in the cation, the anion and cation nature; and interactions between anion and cation. Generally, there is a positive relationship between the alkyl side chain length and toxicity, and an inverse relationship between the relative number of oxygen atoms and toxicity. However, the toxicity of ionic liquids does not always comply with the above rules. The current chemical and biological degradation methods of ionic liquids were reviewed. It is necessary to choose safe and effective degradation methods according to the anions and cations of ionic liquids. Ionic liquids with short side chains should choose chemical degradation as far as possible, while ionic liquids with long alkyl side chains should give priority to biodegradation. In addition, the influences of ionic liquids’ structure on their degradation performance need to be systematically studied. In order to provide a basis for the development of low toxicity and biodegradable ionic liquids, it is also an important way to improve the safety of ionic liquids. This paper clarifies that further study on the environmental behavior, safety effects and degradation methods of ionic liquids is of high scientific value, which is great significance for objective evaluation of the potential of large-scale application of ionic liquids.