Polyelectrolyte (PE) gels consist of crosslinked polymer networks that are grafted with ionizable groups and ionic solution. Many stimuli-responsive gels, including pH-responsive, electric-responsive, and light-responsive ones, are PE gels. Most soft biological components are also PE gels. Due to the increasing scientific interests and applications of PE gels, a comprehensive model is needed. In PE gels, not only solvent, but also ions and other small molecules all diffuse inside, and the flows of the different components are coupled. This phenomenon is called cross-diffusion, meaning the flow of one species is not only driven by its own chemical potential gradient, but also influenced by the flow of other species. In this work, we develop a rigorous nonequilibrium thermodynamics framework to study the coupled deformation and diffusion of the PE gels where cross-diffusion is emphasized and quantified. Specific forms of free energy and kinetic laws are proposed. A finite element method is developed and implemented into abaqus through a user element subroutine. The model is used to simulate the deformation of biological axon and PE gels.The numerical results are compared with experimental data. It is shown that cross-diffusion generates anomalous effects not only on the flux but also on the deformation of PE gels.