To provide a reference to advance related research in China, this article reviews microbial research progress in the deep Arctic, discusses prospects, and makes recommendations for macro-strategies. The rich diversity and enormous genetic resource of deep Arctic micro-organisms is described. In addition, it is determined that microbial communities exist as distinct spatial and stratified distributions and are found to play an important role in the deep Arctic food web. It is of great value to study the diversity and bio-geography of the deep Arctic micro- organisms, identify their novel genetic and biochemical functions, and investigate their roles in multiscale ecosystems related to the global climate change. Therefore, a top-down design including a collaborative innovation system construction and developments of special deep-sea instruments are proposed to accelerate the deep Arctic microbial research in China.