Abstract: China, as the biggest energy consumer with large amounts of CO₂ emissions, is faced with an arduous task and responsibility for carbon emission reduction. According to previous studies, karst carbon sequestration flux has the same magnitude as forest carbon sequestration and soil carbon sequestration in the country. In order to make the best of karst carbon sequestration, it is necessary to further investigate and clarify the influencing factors and mechanisms of karst carbon sequestration, and to improve the estimation accuracy. In this paper, systematic discussions are made on the process of carbon cycle at watershed scale, with the focus on the biological effects of karst carbon cycle, study of the regulations of carbon dioxide recycle in hydrosphere, and assessment of the influence level and promote strength of allogenic water to karstification. By using a mathematical regression model, we estimated the carbon fluxes in karst region to improve the overall estimation precision, and proposed techniques to increase the karst potential carbon sequestration. All of these results provide fundamental support for the scientific estimation of karst carbon sequestration flux in China.