Safety assessments in nuclear waste management typically include the analysis of thermo-mechanical (TM)-coupled processes. The TM behavior of the host rock is, among other aspects, dependent on the prevalent geological geometry. This study aims to evaluate the impact of uncertainties in geometry on the TM rock behavior. It is one of the very first studies aiming to bring uncertainties of structural geological models and numerical simulations together. To analyze the influence of geological geometries, a simplified model of the region around the Mont Terri rock laboratory was created. A 3D structural geological model was set up and uncertainties of the lithological contacts were quantified by means of stochastic simulations, resulting in an ensemble of 89 model realizations. These realizations were transformed to a 2D numerical model. In this numerical model, TM simulations were computed over a simulation time of 500 years, employing the Finite Element Method. To simulate a heat source of nuclear waste, the lower edge of the model was set to 100 °C. The results of these simulations show mean temperature variations of 90.89 and 92.70 °C after 500 years, with a maximum stress varying between 0.02 and 0.16 MPa of elastic shear energy density and according mean cumulative displacements ranging from 30 to 38 cm. The presented results indicate that different model geometries and differences in material properties lead to noticeable variabilities of the TM behavior of claystone. However, in this case, these variabilities would not significantly affect the integrity of the rock.