Hydraulic conductivity is an important parameter to describe the permeability characterization of fractured rock mass. It is often determined using the water pressure tests of borehole in hydraulic and hydro-power engineering. When the water pressure is very low, the permeability variation of rock mass is not obvious owing to its integrity and strength. But under high water pressure, its permeability would change obviously. The main reasons are that fractured apertures can be increased, some close fractures may be re-opened, and the small and unconnected fractures are penetrated between each other under the action of high water pressure. Changes of permeability would lead to some difficulties for seepage analysis, because hydraulic conductivity is often considered to be constant. The calculated hydraulic head and flux have great errors if the variation of permeability coefficient hasn't been considered. On the condition of high water pressure, the relationship between hydraulic conductivity of fractured rock mass and water pressure is deduced according to the Non-Darcy flow equation in this paper. Three equations for calculating hydraulic conductivity are provided here. The first equation is applied to the condition for low water pressure. The results of field water pressure test show that when the hydraulic fracturing of rock mass occurs, hydraulic conductivity increases obviously. It can be calculated through the variation of water flux and water pressure. In this paper, variation characteristics of permeability coefficient before and after hydraulic fracturing are verified using the results of high pressure water test from pumped storage power stations. Field test results are used to calculate hydraulic conductivity of rock mass. A comparison is conducted for measured and calculated hydraulic conductivity values to validate the rationality of deduced equation. The errors between measured and calculated values are less than 15 percent and the average error is about 10 percent, which show the calculated hydraulic conductivity is basically in agreement with measured value. Expressions of hydraulic conductivity provide selection criteria of seepage analysis for hydraulic and hydro-power engineering or large deep tunnel project.