Cyanobacterial toxin is the secondary metabolite produced by cyanobacteria. It has serious toxicity and carcinogenicity to human or terrestrial animals, and it may damage the structure and function of water ecosystems. Environmental and health issues caused by the frequent occurrence of toxic algal blooms have become research hotspots in the field of environmental science. Available water treatment facilities being used nowadays to remove cyanobacterial toxin from drinking water are unsatisfying, so searching an efficient method for removing algal toxin is an urgent issue to be solved. This paper described the production and release mechanism of cyanobacterial toxin firstly, divides the removal methods of cyanobacterial toxin into two categories, as algae removal and the removal of dissolved toxin in water. In addition, current degradation pathways of cyanobacterial toxin were reviewed based on a large number of research results. The details of activated carbon adsorption, advanced oxidation degradation, microbial degradation and other removal methods that have practical application prospects were introduced. Finally, this paper summarized the limitations of current cyanobacterial toxin removal methods, and points out that the future methods should be highly efficient, with low energy consumption, pollution free and practicable.