Cylindrospermopsis raciborskii has gradually spread from the tropic and subtropic regions to temperate regions due to the global warming and water eutrophication. C. raciborskii can dominate in many water bodies and develop blooms, which has received widespread attention. The massive proliferation of C. raciborskii affects community structure and species diversity of local aquatic ecosystem and destroys the balance of ecosystem. Furthermore, the toxic metabolites released from C. raciborskii will pose severe threats to human and other animals via bioaccumulation and food chain transmission. In this review, we systematically evaluated the potential impacts of C. raciborskii invasion and proliferation on the community structure and species diversity of local aquatic ecosystems as well as the underlying mechanism. The impacts of C. raciborskii invasion on aquatic ecosystems not only depended on the characteristics of C. raciborskii strain and its invasive situations, but also were related to the environmental factors and species composition of local aquatic ecosystems. Therefore, ecological consequences of the same C. raciborskii species's invasion can vary spatially and temporally. Under certain environmental conditions, C. raciborskii could affect species composition and biodiversity of native aquatic ecosystems mainly through its strong interspecific competition, ecotoxicity to other aquatic organisms as well as its regulation to aquatic bacterial communities. Finally, future studies were prospected in allusion to some hotspot problems, such as the ecological consequences of invasion, the biotic interactions and the effective prevention and control, which would provide a theoretical basis for comprehensively understanding the impacts of invasion on aquatic ecosystems.