The boundary value problem for the system of quasi-linear parabolic equations in the presence of integral conjugation conditions is considered. The boundary value problem is a mathematical model of the process of non-isothermal filtration consolidation of the soil mass which contains a thin geobarrier. Geobarriers exposed to non-isothermal conditions are a component of waste storage facilities. The change of hydromechanical and thermal properties the geobarriers, as well as the phenomenon of thermal osmosis, require modification of both the equations in the mathematical model and the conjugation conditions. The finite element method is used to find approximate solutions of the corresponding system of quasi-linear parabolic equations. The existence and uniqueness of the approximate generalized solution is proved. The accuracy of finite element solutions in the sense of total approximation are also estimated. The differences in the values of pressure and temperature distributions for the classical case and the case considered in the article were analyzed on the test model example.