For an energy storage application such as electrical vehicles (EVs), lithium-ion batteries must overcome limited lifetime and performance degradation under specific conditions. Particularly, lithium-ion batteries show significant capacity loss at higher discharging rates (C-rates). In this work, we develop computational models incorporating coupled electrochemical-mechanical-thermal factors in order to reveal the relationship between the experimentally observed capacity loss and predicted mechanical stresses during electrochemical (dis)charging. Specifically, a multiphysics finite element model consisting of electrochemistry, heat generation, mass transport, and solid mechanics is developed to investigate thermal- and diffusion-induced stresses with the reconstructed porous microstructures of commercial LiFePO4 batteries. It has been suggested that porous microstructures in electrodes could mitigate the electrolyte reactivity for an improved battery life and safety. Therefore, the reconstructed porous microstructures from Focused Ion Beam-Scanning Electron Microscopy (FIB-SEM) images are adopted. The integrated experimental measurements and computational simulations show that: (1) lithium-ion cells electrochemically tested at 3.6C have 30% capacity loss versus cells tested at 1.2C; a corresponding stress increase of 150% is observed from the multiphysic simulations, (2) the thermal models verified by in operando temperature measurement via the fiber Bragg grating (FBG) sensor demonstrate that increasing temperature results in larger thermal stresses during (dis)charging. However, increases in thermal stress due to higher temperature played a lesser role at higher C-rates, (3) lithium ion concentration distribution is location dependent, that is, at any time and at any given C-rates, the outer layer of the particle exhibits a higher concentration than that inside the particle, and (4) higher diffusion-induced stresses are observed at the connecting areas between particles, suggesting that the higher stresses may result from higher concentration variations in the connecting area. This study presents results that include evolutions of lithium ion concentration and mechanical stresses and could help to provide insight into the decreasing electrochemical performance of lithium-ion batteries at higher C-rates.