Reaction non-uniformity develops in battery electrodes across a wide range of length scales from the electrode to agglomerate and primary particle level. The resultant non-uniform state of charge distribution increases polarization and reduces energy utilization and rate performance. It generates incompatible volume changes, which triggers microcracks and dislocations. Inhomogeneous intercalation could cause overheating at local spots of high current density and also over-charge/discharge, which leads to irreversible structure decomposition and capacity fading. Understanding the origins of reaction heterogeneity and identifying its mitigation strategy is critical for developing better and safer batteries. In this work, we use mesoscale theory and simulation to elucidate a few important factors in the development of non-uniform reaction distribution at different length scales. At the single particle level, we show that misfit stress generated by lattice mismatch between the lithiated and delithiated phases plays an important role in inducing non-uniform (de)intercalation front through two general mechanisms. The first mechanism, referred to as “surface-mode coherent spinodal decomposition”, occurs in systems that undergo spontaneous phase separation such as olivine LiFePO4. We use phase-field simulation to reveal the morphological evolution of intercalation front in LiFePO4 under stress influence, which satisfactorily explains recent in-situ experimental observations. The second mechanism, which we refer to as “inverted Grinfeld instability”, is analogous to the well-known Asaro-Tiller-Grinfeld instability in epitaxial thin film growth and applies to electrode materials such as Li(Ni0.5Mn1.5)O4 with first-order phase transformations upon cycling. We employ linear stability analysis to establish the criteria of interface instability and construct interface stability diagrams in the space of particle size, applied overpotential / flux and interface location, from which the conditions for achieving uniform intercalation can be identified. At the electrode level, we identify electrolyte depletion as a major factor contributing to reaction inhomogeneity especially at large electrode thickness. By analyzing battery (dis)charge kinetics in the framework of porous electrode theory, two types of non-uniform reaction behavior are discovered for electrode systems that exhibit solid-solution-like (e.g. NMC) or phase-changing (e.g. LiFePO4, Li4Ti5O12) intercalation behavior, respectively. A simplified analytical model was developed to quantitatively describe such behaviors, which shows very good agreement with numerical simulations and provides an efficient tool for predicting reaction distribution within composite electrodes. We further elucidate the coupled effects of ionic and electronic conductivities and surface reaction kinetics on reaction uniformity through a simplified circuit model. Based on the theoretical understanding, we suggest that balancing the kinetic competition between electrolyte transport, electronic conduction and surface reactions represents an effective strategy to promote homogeneous reaction in thick battery electrodes.