Abstract: Carbon cycling acts a vital role in the global exchange of substance and energy flow, influencing climate change dynamics. The carbon cycling process in freshwater ecosystem is an important component of global carbon cycling. Therefore, studying carbon storage and emission processes in freshwater ecosystems can increase our understanding of carbon cycling processes in freshwater ecosystems. In addition, investigating the influencing factors can provide theoretical basis for formulating the relevant measures to mitigate and manage global warming. This paper first reviews the roads of sediment carbon storage and emission in freshwater ecosystems, and then discusses the influence factors of carbon storage and emission from climatic conditions, hydrologic conditions (water level, water quality and temperature), and biological factors (phytoplankton, microorganism, aquatic animals and submerged macrophytes) under the background of global climate warming. These factors not only interact and correlate with each other but also directly and indirectly affect carbon storage and emission of sediment. The variation of carbon storage and emission of sediment is account for the composite effects of many factors. In conclusion, this paper looks forward to the prospects of how to implement increasing of carbon sequestration in freshwater ecosystems.