This paper describes the coupling analysis of thermo-mechanical consolidation and its discretization method to simulate the seepage flow due to heat and deformation of nuclear waste storage on jointed rock mass by finite element method. The authors followed basic equations presented by Ohnishi et al. (1986) and an anisotropic stress-strain and permeable constitutive laws are employed for combining arbitrary oriented joint sets by compliance matrixes (T. F. Cho, 1988). Four node standard iso-parametric finite element as Sandhu 1-1 type with reduced integration and scaling method are employed for the stabilities of numerical calculations. The results of two dimensional rock mass models with combining arbitrary oriented joint sets show that the direction of fluid flow is followed along the joint sets, and those are seemed to be clearly explained of the influence of joint orientations.