The rapidly increasing demand for efficient energy storage systems in the last two decades has stimulated enormous efforts to the development of high-capacity, high-power, durable lithium ion batteries. Inherent to the high-capacity electrode materials is material degradation and failure due to the large volumetric changes during the electrochemical cycling, causing fast capacity decay and low cycle life. This review surveys recent progress in continuum-level computational modeling of the degradation mechanisms of high-capacity anode materials for lithium-ion batteries. Using silicon (Si) as an example, we highlight the strong coupling between electrochemical kinetics and mechanical stress in the degradation process. We show that the coupling phenomena can be tailored through a set of materials design strategies, including surface coating and porosity, presenting effective methods to mitigate the degradation. Validated by the experimental data, the modeling results lay down a foundation for engineering, diagnosis, and optimization of high-performance lithium ion batteries.