In order to meet the requirements of ultra-low flue gas emission, the desulfurization system of 660 MW coal-fired unit was upgraded to increase its capacity and efficiency. Applying mixed combustion of economical coals, the economic efficiency of the desulfurization system was analyzed by changing the load and sulfur content of coal. The calculation models were established based on desulfurization performance, desulfurization cost per unit power supply, and hourly average operation cost. The operation cost and potential of the desulfurization system were analyzed. The results showed that, when the unit operated at 100% load and met the ultra-low emission requirements, the maximum SO2 content of raw flue gas that the desulfurization system could with stand was 2 320 mg/Nm3, which equaled to a coal sulfur content of 1.1%. When the sulfur content of coal in furnace was greater than 0.85%, the hourly average desulfurization cost increased rapidly. When the sulfur content of coal in furnace increased to more than 1.1%, all equipments of the system operated at full capacity, with lack of redundancy and poor reliability. The desulfurization system had a good performance in economy and reliability when the the sulfur content of coal in furnace was 0.66%~0.85%.