Agriculture is one of the main sources of anthropogenic greenhouse gases on the earth, but it also serves as a carbon sink, which has great potential for greenhouse gas absorption. Based on the scientific calculation system of carbon emissions and carbon sinks in agriculture, we calculated the carbon emissions and carbon sinks of agriculture using data from Hotan Prefecture for the period 1999-2014. The results showed that the net carbon sink (total carbon sinks and total carbon emissions) showed a stable increase trend in Hotan during 1999-2014. The carbon sinks level of agriculture in Hotan prefecture is more than three times of that in China and more than two times that in Xinjiang. Thus, the agricultural carbon sinks function of Hotan is obvious. To realize sustainable agricultural development and to transform agricultural carbon sinks into the power to promote regional economic development, we established the ecological compensation mechanism of agricultural carbon sinks from the aspects of the main body of compensation, compensation principle, compensation method, and compensation standard within the premise of the ecological function of carbon sinks in agriculture. We use the net carbon sinks amount multiplied by the unit price of carbon sinks to obtain the amount of agricultural carbon sinks compensation in this paper. Compensation methods include government compensation and market compensation. Government compensation mainly comprises financial, material, policy, and technical compensation. Market compensation mainly uses the carbon trading platform to compensate for the net carbon sinks of agriculture.