Abstract: Abstract: Identifying and predicting the evolutionary characteristics of ecosystem communities under environmental changes is the critical prerequisite for formulating aquatic ecosystem management and protection strategies. However, due to the lack of long-term ecological monitoring data, there are still many deficiencies in how to effectively reveal the evolution of species and communities in the ecosystem. Using the historical natural resource archives of species stored in sediment ancient DNA to detect and interpret ancient DNA information will improve our understanding of species migration and extinction, community evolution dynamics, ecosystem structure and function changes driven by environmental changes. First, this study focuses on the technical principles and development of ancient DNA; then, the application of ancient DNA in eco-environment fields was summarized, including species invasion and colonization, species genetic diversity, community evolution and revealing the characteristics of long-term changes of ecosystems under environmental stressors; finally, the potential solutions were proposed for the existing problems and defects of sediment ancient DNA technology, which is expected to provide new technologies and pathways for the reconstruction of biological communities in aquatic ecosystems based on sediment ancient DNA.