Environmental DNA metabarcoding is defined as high throughput DNA sequencing used for simultaneous molecular identification of multiple taxa in a complex environmental sample (i.e., soil, water, feces, etc.). In recent years, this method has aroused widespread concern among scientists and has been increasingly used in the field of ecology, such as biodiversity research, monitoring of aquatic, rare, or invasive species. This article describes the significance and the methods of environmental DNA metabarcoding, and highlights its application in the fields of species monitoring,detection of rare and invasive species, biodiversity, and diet analysis. Finally, this article summarizes the challenges in application of environmental DNA metabarcoding in ecological research and discusses the future prospects of its development.