As a common prokaryote in the deep subsurface biosphere, archaea are widely distributed in various marine sedimentary habitats and play important roles in the biogeochemical cycles. Due to the differences in physiological adaptabilities of different archaeal groups to environmental conditions, they constitute anaerobic microbial ecosystem and aerobic microbial ecosystem in coastal and open ocean sediments, respectively. In this paper, we compare the archaeal community structure in two different dimensions:nearshore and ocean, sediment and overlying water, and discuss the distribution, metabolism and environmental adaptation mechanism of common archaea (Thaumarchaeota, Bathyarchaeota, Thermoprofundales, Asgard, Woesearchaeota) in deep subsurface biosphere. We summary the research progresses of archaea in the deep subsurface biosphere. We also put forward several future research directions and key points of archaea for references.