Fractured rocks are a type of complex media that widely exist in various projects including energy, hydraulic, and underground space engineering, whose permeability properties are a hotspot in current rock mechanics domain. Aiming at investigating the seepage characteristics of the fracture surfaces in different rock strata, uniaxial compressive test and permeability test were performed on single-fracture homogenous and heterogeneous rocks. Specifically, rock’s physical and mechanical parameters were measured in uniaxial tests while the initial width of the single fracture was determined through CT scanning. In combination with test results and the calculation model of the displacement of single-fracture heterogeneous rock under triaxial stress condition, the calculation formula of the permeability coefficient of single-fracture heterogeneous rock was derived. Results show that hydraulic pressure in the fracture can affect the permeability coefficient of the fractured rock. Hydraulic fracturing effect occurred with the increase of hydraulic pressure in the fracture, which then generates slight normal deformations of the rock masses on both two sides of the fracture surface, decreases the contact area in the fracture, and leads to the increases of both fracture width and permeability coefficient. For single-fracture rock, the lithological properties of the rock masses on both two sides of the fracture surface impose significant effects on the permeability coefficient. Under same hydraulic pressure and confining pressure, the permeability coefficient of single-fracture coarse sandstone is greatest, followed by that of single-fracture heterogeneous rock, and finally by single-fracture fine sandstone. Theoretical calculation results agree well with the test results, suggesting that the derived theoretical formula can adequately describe the variation tendencies of permeability coefficient with confining pressure and hydraulic pressure in the fracture.