A "sofigenthcarbon formation" is a subsurface pool of hydrocarbons contained in the rock formations that can be easily broken into irregular fractured bodies when the mechanical environment changes. Typically, it happens on low overall strength rocks with anisotropic property of seepage and stress, such as coal, carbonate, unconsolidated sandstone or fractured tight sandstone, shale. Due to the strong heterogeneity of fractured reservoirs in the vertical direction, it is difficult to reflect the overall reservoir damage degree caused by working fluids by testing the permeability change of a single core plug before and after the intrusion of working fluids. To this end, this paper took advantage of the Darcy's law to theoretically discuss the feasibility of replacing the permeability with the flow rates to quantitatively characterize the reservoir damage degree. Then, the flow test experiments were carried out on single-layer development, double-layer joint development and three-layer joint development to evaluate the overall damage degree of single-layer and multi-layer reservoirs by working fluids. Finally, the flow damage degree was compared with the permeability damage degree to verify the feasibility of replacing permeability with flow rates. And the following research results were obtained. First, during the single-layer development, the flow-rate damage and the permeability damage are basically accordant, and the permeability damage degree is a special form of the flow-rate damage degree. Second, during the double-layer and three-layer joint development, the steady flow-rate damage degree of each layer is close to the permeability damage degree, and the flow-rate damage rate can quantitatively characterize the overall damage degree of jointly developed reservoirs, but the permeability damage degree cannot. Third, the steady flow-rate damage degree is closer to the permeability damage degree than the cumulative flow-rate damage degree. In conclusion, the determination of steady flow rates can be used as the substitute of permeability measurement to evaluate the damage degree of fractured reservoirs by working fluids, so as to provide a method and a basis for optimizing the engineering technology and evaluating the adaptability of working fluids.