The PVC-P geomembrane in the impervious structure of high membrane faced rockfill dams has excellent impermeability. However, it has large elongation at the peripheral joints due to differential displacement, which is the weak section of the impervious system. To identify whether the permeability of PVC-P geomembrane in tensile deformation meets the engineering requirements during the operation, a series of permeability tests at several elongations were carried out by a self-developed permeability tester for geomembrane in tensile deformation, and the microscopic permeability of PVC-P geomembrane in tensile deformation microscopically was explored by low-field nuclear magnetic resonance (NMR) technology. The results show that the impermeability of PVC-P geomembrane decreases, and the permeability coefficient increases with the increase of elongation; which causes the development of pore throats, the increase of content and the enhancement of pore-throat connectivity within the geomembrane, which is the essential reason for the decrease of the impermeability. The results show that the PVC-P geomembrane in tensile deformation still has a low permeability coefficient, however, it has complicated tensile deformation at the peripheral joints of the high membrane faced rockfill dam, which may cause local damages or breakage of the geomembrane. Consequently, it is recommended to take engineering measures to reduce the elongation to prolong the service life.