The Third Pole (TP) is the largest alpine mountains on the Earth. Its cryosphere is shrinking and collapsing and the hydrosphere has subsequently changed under the warming climate in recent decades, potentially affecting the biogeochemical cycle. In particular, the carbon cycle has undergone dramatic changes, primarily because of the alterations between the cryosphere and hydrosphere. Carbon emissions from melting glaciers and thawing permafrost can trigger climate change feedback. However, carbon dynamics linked to the changes of cryosphere and hydrosphere under climate warming on the TP still require clarification comprehensively. Herein, we reviewed the current state of carbon stocks in the changing TP cryosphere and hydrosphere, focusing on their variations in permafrost, glaciers, and related inland waters (headwater rivers, thermokarst lakes, and glacial lakes). We also revealed the carbon release pathways into aquatic ecosystems and the atmosphere. Finally, we recommended research priorities to address the dynamics of carbon cycling and its possible future impacts on the TP. This review highlights the importance of carbon cycle dynamics in the TP under future climate change.