We investigate the non-isothermal non-Newtonian filling process according to the phase field method in three dimensions. The moving interface between the Newtonian and non-Newtonian fluid is captured by the Cahn-Hilliard equation. Based on phase field parameters, the governing equations of the flow field could be written in a unified form. After that, the Navier-Stokes equations are split into several sub-equations and the FEM and SUPG will be used to handle the appropriate equations. The variation of the viscosity of the polymer melt is described via the Cross-WLF model. The thin wall rectangular cavities with and without obstacles are considered to illustrate the convergence, robustness and accuracy of the numerical algorithm. The influences of the inlet velocity and the size of the injection gate on the filling process are analyzed. The numerical results agree well with the experimental data and also exhibit good mass conservation properties.