In all earth ecosystems, the coastal zone is one of the most active areas in multiple biogeochemical cycles. As the major driver of natural biogeochemical cycles, microbial community in coastal ecosystems is of vital importance to the material transformation and energy flow in this critical zone. In this review, we summarized the responses and feedbacks of microbial community to the circumstances of climate change and anthropogenic disturbance in typical coastal areas, such as coastal wetlands, offshore waters, seagrass meadows and kelp forests. It was mainly elucidated around microbes-involved carbon and nitrogen cycles, and greenhouse gases emission to reveal the microbial mechanisms on coastal ecosystem functioning and maintenance. Finally, some preliminary prospects are provided for the future studies of microbial ecology in the coastal zones.