With the rapid growth of new energy and renewable energy, and the declining utilization hours of thermal units, a lot of thermal power units have been used for deep peak regulation even reserve ancillary service. The survival of thermal power enterprises is threatened. However, the moderate thermal power units are needed to ensure the safety and stability of power system. So it is urgent to research the reasonable compensation methods for the thermal power enterprises. Considering that electricity market is high relative to carbon exchange market, compensation mechanism based on electricity-carbon linkage is proposed. A comprehensive compensation method including carbon compensation is put forward to make up for the rights and interests of power generation abandoned by the thermal power enterprises. On the background of Yunnan power market, an example is calculated to demonstrate theSeffectiveness of the proposed method.