A fluid flowing through fractured rock masses has complex characteristics, and the fracture permeability of these rock masses is an essential parameter to evaluate the capacity of the fluid. In this work, five groups of fractured limestone samples with different joint roughness coefficient (JRC) were prepared using an innovative method. The effects of the JRC, filling fracture width (Be), permeating solution, and confining and seepage pressures on the fracture permeability characteristics of limestone were investigated. The variation pattern of the fracture surface morphology was revealed, and the evolution of the fracture permeability of limestone was discussed. At constant confining and seepage pressures, the fracture permeability exhibited three distinct evolution stages with time: rapid decline, gradual decline, and stabilization. The stable value of the fracture permeability showed logarithmic and linear relationships with the JRC and Be, respectively. Further, the results of permeability tests conducted on fractured limestone samples immersed in a sodium sulfate solution showed an increase in JRC from 2.50% to 36.61% for different fracture surfaces and a decrease in the sample permeability. The fracture permeability of the samples with different JRCs decreased with increasing pressure. There was a significant hysteresis effect during the unloading of the confining pressure. The loading and unloading of the seepage pressure reduced the fracture surface permeability at a confining pressure of 3.0 MPa and in the seepage pressure range of 0.2–1.5 MPa. This study provides a theoretical basis for estimating the fracture permeability of limestone and similar rocks.