Climate warming caused by the increase in atmospheric greenhouse gas concentration has brought serious impact on the sustainable development of human society. The hydrospheric ecosystem is not only one of the world's most important carbon sinks, but also the world's most important natural sources of methane emissions. Therefore, understanding of hydrospheric methane emission and related microbial mechanisms under climate warming is important to reveal the future trend of the earth's climate system and predict potential scenarios of future global change. Additionally, it will provide basic theoretical support for how to effectively utilize the potential of the carbon sink in the hydrosphere, in order to better respond to global climate change issues. In this paper, we review the status and trend of microbial-mediated methane emissions of the main hydrospheric ecosystems under climate warming, and introduce the complex regulatory effects of climate warming on microbial communities and functions related to methane metabolisms. In view of the current research status, it is urgent to carry out related researches based on the complexity of ecosystems and the long-term nature of climate warming through a combination of micro-mechanisms and macro-processes. Meanwhile, it is suggested to strengthen the researches in relatively weak areas such as the ocean.