Methane is a more active greenhouse gas than CO2, and the process of methane anaerobic oxidation (AOM) driven by microorganisms is of great significance in reducing global methane emissions. The final electron acceptors involved in AOM reaction are mainly divided into three categories: sulfate, nitrite/nitrate, and metal ions represented by Fe(III), Mn(IV), etc. Both soluble metal substances and insoluble metal minerals can be used as electron acceptors for AOM, which greatly enhances the ecological value of microorganisms participating in metal-dependent anaerobic oxidation of methane (Metal-AOM). The current research focuses on functional flora, ecological distribution, etc. Some anaerobic methanotrophic archaea (ANME) have the ability to participate in Metal-AOM process directly or indirectly. However, due to the difficulty in purification, enrichment and isolation of functional microorganisms, the study on their physiological, biochemical and ecological characteristics has been limited. Meanwhile, with the discovery of Metal-AOM in different aquatic habitats, its application in the field of pollution control has been widely discussed; but there is a lack of in-depth research of estuarine habitats. Based on the discovery of Metal-AOM, the main microorganisms involved in the process and their ecological distribution in the aquatic environment were described, and the reaction mechanism of Metal-AOM and its opportunities and challenges in practical application were introduced. Finally, based on the existing research results, this paper puts forward the research prospects of functional microflora, mechanisms and environmental applications, including the isolation and purification of microorganisms, the analysis of their metabolic activity and mechanism of action, as well as the design, development and application of new production techniques, in order to provide reference for environmental pollution control and industrial applications in the future.