The impervious system of cofferdam, which is composed of composite geomembrane and impervious wall, is easily damaged at the joint parts. In view of this, the pattern of joint between composite geomembrane and impervious wall needs to be studied in order to insure the safety of the whole cofferdam and to avoid the damage of geomembrane caused by the deformation difference between cofferdam body and impervious wall. A case study on the high earth-rockfill cofferdam of a hydropower station in west China was carried out by means of nonlinear finite element method. The research focused on the stress and deformation behaviors of the geomembrane and the high cofferdam built on deep overburden. Results show that the joint pattern had little influence on the stress and deformation of dam body and impervious wall, but had significant influence on the geomembrane strain and the deformation difference between dam body and impervious wall. If the geomembrane is laid horizontally on the top of impervious wall, the settlement difference could induce large tensile strain of geomembrane at joint parts. With the rising of the location of geomembrane, the tensile strain decreased remarkably, which is beneficial for its safety. In conclusion, it is reasonable to lay the geomembrane above the impervious wall for a distance. The critical thickness of overlaying soil should be determined by indoor pull-out tests.