Under the restriction of ultra-low emission of flue gas pollutants, the large-scale circulating fluidized bed generator sets can not meet the requirements by desulfurization in the furnace lonely, and need to use a flue gas desulfurization system outside the furnace. The organic matching of the two desulfurization can reduce the comprehensive desulfurization cost. The optimal desulfurization distribution ratio of two-stage combined deep desulfurization in the operation process of power plant can achieve the lowest desulfurization cost under the emission standard. According to a variety of cost factors, a technical and economic calculation model was established to analyze the influence of different furnace calcium-sulfur ratios on the desulfurization distribution ratio and main cost factors, and explore the impact of different limestone prices and plant electricity prices on the comprehensive desulfurization cost. The results show that when the ratio of calcium to sulfur in the furnace is 1.0, 1.1-1.5, 1.6, 1.7-2.1, the best desulfurization shares in the furnace are 70%, 60%, 85% and 80%, respectively. Furnace desulfurization has great influence on boiler thermal efficiency, and the higher the molar ratio of calcium to sulfur, the greater the influence. When the ratio of calcium to sulfur exceeds 2.0, the heat loss of in-furnace desulfurization can reduce boiler thermal efficiency. The main cost factors of in-furnace desulfurization are limestone powder cost and operation power consumption cost, and the main cost factors of limestone/gypsum wet flue gas desulfurization are limestone slurry cost and absorption tower operation power consumption cost, which have obvious changes with different desulfurization distribution ratio. Different limestone prices and factory electricity prices have different optimal desulfurization distribution shares under different conditions of calcium-sulfur ratio in the furnace.