This paper discusses numerical simulation of three-dimensional compressible contamination treatment from nuclear waste in porous media. The mathematical model includes five major unknowns, the pressure, Darcy velocity, brine, radionuclide and the temperature, determined by a parabolic equation, convection-dominated diffusion equations and the heat conductor equation. Considering the physical properties and the characters of equations, a mixed volume element with the characteristics is presented. For the flow equation, a conservative mixed volume element is used to obtain the pressure and Darcy velocity, and improves the accuracy of the latter. The characteristics could solve the convection dominated problems well and confirm the stability and accuracy at the front sharps, thus a characteristic mixed volume element is given for computing the concentrations and temperature. The composite procedures have the nature of conservation. Convergence analysis is discussed. Finally, an experimental system of partial differential equations is carried out and the feasibility and computational efficiency are illustrated. This method could solve such complicated problems well.