The decline of global fisheries is one of the major challenges in the 21st century. In recent years, global fish diversity has declined dramatically under the influence of human activities. In order to effectively curb the decline of fish resources, the accurate fish ecological surveys are the top priority. Traditional fish monitoring is based on catch collection and morphological identification, which is often time-consuming and ineffective, and can no longer meet the needs of accurate surveys at large scales. As an emerging method of fish ecological survey in recent years, environmental DNA technology has the advantages of high sensitivity, low technical threshold, cost-effective, small sampling limitation and no disturbance to the ecosystem compared with the traditional methods. Environmental DNA is the total DNA of all organisms obtained from environmental samples such as water, sediment, soil, and air that have not been pre-isolated. At present, environmental DNA technology has been widely applied in the research of fish species monitoring, diversity survey, biomass assessment, spawning activity monitoring, population genetic analyses, fish feeding analyses and ecological health evaluation. However, some problems exposed in the specific application of environmental DNA technology in fish ecology studies can affect the accuracy of its monitoring results, such as the irregularity of the operation procedure, the incompleteness of the genetic database, and the unclear ecological processes of environmental DNA in the environment. In order to be able to obtain more credible results from environmental DNA technology, researchers must have an accurate grasp of the developments in environmental DNA technology. Therefore, this paper firstly reviews the development history of environmental DNA technology, the analysis process and the research progress of environmental DNA technology in the field of fish ecology research. Then, we focus on the current difficulties and challenges faced by the development of environmental DNA technology and propose the corresponding solutions. Finally, an outlook is given on the future development trend of environmental DNA technology in the field of fish ecology research. Although environmental DNA technology has been widely used worldwide, its development in China is still in the preliminary stage. We aim to provide a theoretical foundation for the accurate application of environmental DNA technology in the field of fish ecology in China. It is believed that in the near future, environmental DNA technology will be able to develop significantly in the field of fish ecology, and is expected to become a routine tool for fish resources survey.