Current prototypes of lithium-ion batteries lose capacity at high C-rate cycling. It is one of the paramount obstacles hindering many potential emerging technologies ranging from power tools and portable electronics to recent PHEV/EV. Recent studies show that electrodes’ stresses and deformations play a significant role in rate-capacity loss, suggesting that coupling effects exist between the mechanical energy, electrochemical transport process, and electrical potential and capacity. Current available models capturing such coupling effects are developed for specific cases, however. Such as models with idealized geometries, linear deformation or isotropic material properties, resulting the irreversible capacity loss found in experiments was inaccurately described. In this study, nonequilibrium thermodynamics and field equations are incorporated, in which nonlinear deformation and anisotropy material properties are included in the model. With that, one could systematically analyze and investigate phenomena between stress-induced rate capacity fade, phase transformation of anisotropic crystal cathodes, and large deformation on alloy anode for Li-ion batteries. The developed model can be embedded into finite element analysis algorithms to provide a design tool for nanostructure optimization. This research will help understand more details on electrodes’ mechanical behaviors, their influences on transport process in electrodes, and strategies for improving batteries’ high C-rate performance and supplying better lifetime management.