The invention discloses a method and a system for treating desulfurization wastewater. The method comprises the following steps: adding a first reactant into the desulfurization wastewater and performing first-level homogenous softening reaction; performing first-level clarification on the desulfurization wastewater after the first-level homogenous softening reaction in the manner of tubular microfiltration; adding a second reactant into the desulfurization wastewater after the first-level clarification and performing second-level homogenous softening reaction; performing third-level softening reaction; and performing second-level clarification. According to the method for treating desulfurization wastewater provided by the invention, the homogenous softening and clarification for the wastewater are realized through the steps of three-level softening reactions and two-level clarifications, so that the content of the elements, such as, calcium and magnesium in the wastewater can be effectively reduced, the influence of the scales on the subsequent treating equipment can be reduced, the sulfate radicals in the desulfurization wastewater can be reduced at high proportion, the processes of subsequent salt separation and salt crystallization can be simplified, the condition for realizing the zero emission of the desulfurization wastewater of the power plant can be created, the investment and running cost of the zero emission system can be saved and the method has important economic benefit and environmental benefit.